All Publications


 284S.Wang, U.B.Choi, J.Gong, X.Yang, Y.Li, A.L.Wang, X.Yang, A.T.Brunger, C.Ma. Conformational change of syntaxin linker region induced by Munc13s initiates SNARE complex formation in synaptic exocytosis.EMBO J.,10.15252/embj.201695775 (2017).


 283J.Gong, Y.Lai, X.Li, M.Wang, J.Leitz, Y.Hu, Y.Zhang, U.B.Choi, D.Cipriano, R.A.Pfuetzner, T.C.Sudhof, X.Yang, A.T.Brunger, J.Diao (2016). C-terminal domain of mammalian complexin-1 localizes to highly curved membranes. Proc. Natl. Acad. Sci. DOI: 10.1073/pnas.1609917113 (2016).
 282A.Y.Lyubimov, M.Uervirojnangkoorn, O.B.Zeldin, Q.Zhou, M.Zhao, A.S.Brewster, T.Michels-Clark, J.M.Holton, N.K.Sauter, W.I.Weis, and A.T.Brunger (2016). Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Elife 5 e18740 (2016).
 281D.C.Martinelli, K.S.Chew, A.Rohlmann, M.Y.Lum, S.Ressl, S.Hattar, A.T.Brunger, M.Missler, T.C.Sudhof (2016). Expression of C1ql3 in Discrete Neuronal Populations Controls Efferent Synapse Numbers and Diverse Behaviors. Neuron 91, 1034-1051 (2016).
 280J.-P.Colletier, M.R.Sawaya, M.Gingery, J.A.Rodriguez, D.Cascio, A.S.Brewster, T.Michels-Clark, R.H.Hice, N.Coquelle, S.Boutet, G.J.Williams, M.Messerschmidt, D.P.DePonte, R.G.Sierra, H.Laksmono, J.E.Koglin, M.S.Hunter, H-W.Park, M.Uervirojnangkoorn, D.K.Bideshi, A.T.Brunger, B.A.Federici, N.K.Sauter, D.S.Eisenberg. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Nature 539 43-47 (2016).
 279Y.Lai, U.B.Choi, Y.Zhang, M.Zhao, R.A.Pfuetzner, A.L.Wang, J.Diao, A.T.Brunger. N-terminal domain of complexin independently activates calcium-triggered fusion. Proc. Natl. Acad. Sci. USA 113, E4698-E4707 (2016).
 278S.Malmersjo, S.D.Palma, J.Diao, Y.Lai, R.A.Pfuetzner, A.L.Wang, M.A.McMahon, A.Hayer, M.Porteus, B.Bodenmiller, A.T.Brunger, T.Meyer. Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion, EMBO J. 35, 1810-1821 (2016).
 277U.B.Choi, M.Zhao, Y.Zhang, Y.Lai, A.T.Brunger. Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex. Elife 5 e16886 (2016).
 276A.Y.Lyubimov, M.Uervirojnangkoorn, O.B.Zeldin, A.S.Brewster, T.D.Murray, N.K.Sauter, J.M.Berger, W.I.Weis, A.T.Brunger. IOTA : integration optimization, triage and analysis tool for the processing of XFEL diffraction images. J Appl Crystallogr49, 1–8 (2016).
 275J.Lin, H.van den Bedem, A.T.Brunger, M.A.Wilson. Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca2+-calmodulin. Acta Crystallogr D 72, 83–92 (2016).
 274I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.D.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori,T. Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, Lichtenberg, L.Vo Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.S.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Brauer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, T.J.Lane, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano. Structure of photosystem II and substrate binding at room temperature. Nature 540, 453-457 (2016).
 273C.-X.Song, J.Diao, A.T.Brunger, S.R.Quake. Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation. Proc Natl Acad Sci 113, 4338–4343 (2016).
 272E.L.Baxter, L.Aguila, R.Alonso-Mori, C.O.Barnes, C.A.Bonagura, W.Brehmer, A.T.Brunger,..., A.E.Cohen. High-density grids for efficient data collection from multiple crystals. Acta Crystallogr D 72, 2–11 (2016).
 269M.Zhao, A.T.Brunger. Recent Advances in Deciphering the Structure and Molecular Mechanism of the AAA+ ATPase N-Ethylmaleimide-Sensitive Factor (NSF). J.Mol.Biol.428, 1912-1926 (2016)


 271Q.Zhou, Y.Lai, T.Bacaj, M.Zhao, A.Y.Lyubimov, M.Uervirojnangkoorn, O.B.Zeldin, A.S.Brewster, N.K.Sauter, A.E.Cohen, S.M.Soltis, R.Alonso-Mori, M.Chollet, H.T.Lemke, R.A.Pfuetzner, U.B.Choi, W.I.Weis, J.Diao, T.C.Sudhof, A.T.Brunger, Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Nature 525, 62-67 (2015).
 270M.Zhao, S.Wu, Q.Zhou, S.Vivona, D.J.Cipriano, Y.Cheng, A.T.Brunger. Mechanistic insights into the recycling machine of the SNARE complex. Nature 518, 61-67 (2015).
 268M.Uervirojnangkoorn, O.B.Zeldin, A.Y.Lyubimov, J.Hattne, A.S.Brewster, N.K.Sauter, A.T.Brunger, W.I.Weis. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. eLife 4, e05421 (2015).
 267T.D.Murray, A.Y.Lyubimov, C.M.Ogata, H.Vo, M.Uervirojnangkoorn, A.T.Brunger, J.M.Berger. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions. Acta Cryst. D71, 1987-1997 (2015).
 266A.Y.Lyubimov, T.D.Murray, A.Koehl, I.E.Araci, M.Uervirojnangkoorn, O.B.Zeldin, A.E.Cohen, S.M.Soltis, E.L.Baxter, A.S.Brewster, S.N.Sauter, A.T.Brunger, J.M.Berger. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. Acta Cryst. D71, 928-940 (2015).
 265S.Ressl, B.K.Vu, S.Vivona, D.C.Martinelli, T.C.Sudhof, A.T.Brunger. Structures of C1q-like proteins reveal unique features among the C1q/TNF superfamily. Structure 23, 688-699 (2015).
 264Y.Zhang, J.Diao, K.N.Colbert, Y.Lai, R.A.Pfuetzner, M.S.Padolina, S.Vivona, S.Ressl, D.J.Cipriano, U.B.Choi, N.Shah, W.I.Weis, A.T.Brunger. Munc18a does not alter fusion rates mediated by neuronal SNAREs, synaptotagmin, and complexin. J. Bio. Chem. 290, 10518-10534 (2015).
 263J.Diao, R.Liu, Y.Rong, M.Zhao, J.Zhang, Y.Lai, Q.Zhou, L.M.Wilz, J.Li, S.Vivona, R.A.Pfuetzner, A.T.Brunger, Q.Zhong. ATG14 promotes membrane tethering and fusion of autophagosomes to endolysosomes. Nature 520, 563-566 (2015).
 262D.A.Keedy, L.R.Kenner1, M.Warkentin, R.A.Woldeyes, J.B.Hopkins, M.C.Thompson, A.S.Brewster, A.H.Benschoten, E.L.Baxter, M.Uervirojnangkoorn, S.E.McPhillips, J.Song, R.Alonso-Mori, J.M.Holton, W.I.Weis, A.T.Brunger, S.M.Soltis, H.Lemke, A.Gonzalez, N.K.Sauter, A.E.Cohen, H.Bedem, R.E.Thorne, J.S.Fraser. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife 4, e07574 (2015).
 261O.B.Zeldin, A.S. Brewster, J.Hattne, M.Uervirojnangkoorn, A.Y.Lyubimov, Q.Zhou, M.Zhao, W.I.Weis, N.K.Sauter, A.T.Brunger. Data Exploration Toolkit for serial diffraction experiments. Acta Cryst. D71, 352-356 (2015).
 260A.T.Brunger, D.J.Cipriano, J.Diao. Towards reconstitution of membrane fusion mediated by SNAREs and other synaptic proteins. Critical Reviews in Biochemistry and Molecular Biology 50, 231-241 (2015)
 259P.Emsley, A.T.Brunger, T.Lutteke.Tools to assist determination and validation of carbohydrate 3D structure data. Methods in Molecular Biology 1273, 229-240 (2015)


 258T.Tsetsenis, A.A.Boucard, D.Arac, A.T.Brunger, and T.C.Südhof. Direct Visualization of Trans-Synaptic Neurexin–Neuroligin Interactions during Synapse Formation. J. Neurosci. 34, 15083-15096 (2014).
 257A.E.Cohen, M.Soltis, A.González, L.Aguila, R.Alonso-Mori, C.O. Barnes, E.L.Baxtera, W.Brehmer, A.S.Brewster, A.T.Brunger, G.Calero, J.F. Chang, et al. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc. Natl. Acad. Sci USA , 17122-17127 (2014).
 256G.F.Schroder, M.Levitt, A.T.Brunger. Deformable elastic network refinement for low-resolution macromolecular crystallography. Acta Cryst. D70, 2241-2255 (2014).
 255Y.Lai, J.Diao, D.J.Cipriano, Y.Zhang, R.A.Pfuetzner, M.S.Padolina, A.T.Brunger. Complexin inhibits spontaneous release and synchronizes Ca2+-triggered synaptic vesicle fusion by distinct mechanisms. eLife 3, e03756 (2014).


 254A.T.Brunger, P.Strop, M.Vrljic, M.Bowen, S.Chu, and K.R.Weninger. Macromolecular Models by Single Molecule FRET. In: J.D. Puglisi and M.V. Margaris (eds.), Biophysics and Structure to Counter Threats and Challenges, NATO Science for Peace and Security Series B: Physics and Biophysics. 1-19 (2013).
 253T.C.Terwilliger, R.J.Read, PD.Adams, A.T.Brunger, P.V.Afonine, and L.-W.Huang. Model morphing and sequence assignment after molecular replacement. Acta Cryst. D69, 2244-2250 (2013).
 252J.Diao, D.J.Cipriano, M.Zhao, Y.Zhang, S.Shah, M.S.Padolina, R.A.Pfuetzner, and A.T Brunger. Complexin-1 enhances the on-rate of vesicle docking via simultaneous SNARE and membrane interactions. J. Am. Chem. Soc.135, 15274-15277 (2013).
 251S.Vivona, D.Cipriano, S.O’Leary, Y.H.Li, T.D.Fenn, and A.T.Brunger. One NSF, different SNARE complexes: a conserved, t-SNARE-dependent molecular mechanism. J. Biol. Chem,288, 24984-24991(2013).
 250A.Pertsinidis, J.Mukherjee, M.Sharma, Z.P.Pang, S.R.Park, Y.Zhang, A.T.Brunger, T.C.Südhof, and S.Chu. Ultra-high resolution imaging reveals formation and preponderance of neuronal SNARE/Munc18 complexes in situ. Proc. Natl. Acad. Sci. USA, E2812-E2820, doi: 10.1073/pnas.1310654110 (2013).
 249D.J.Cipriano, J.Jung, S.Vivona, T.D.Fenn, A.T.Brunger, Z.Bryant. Processive ATP-driven disassembly of SNARE complexes by the N-ethylmaleimide sensitive factor molecular machine. J. Biol. Chem. 288, 23436-23445 (2013).
 248J.Diao, J.Burre, S.Vivona, D.J.Cipriano, M.Sharma, M.Kyoung, T.C.Sudhof, A.T.Brunger. Native α-synuclein induces clustering of synaptic-vesicle mimics via binding to phospholipids and synaptobrevin-2/VAMP2. eLife 2, e00592 (2013)
 246J.Diao, M.Zhao, Y.Zhang, M.Kyoung, A.T.Brunger. Studying protein-reconstituted proteoliposome fusion with content indicators in vitro. BioEssays 35, 658-665 (2013).
 245P.D.Adams, D.Baker, A.T.Brunger, R.Das, F.DiMaio, R.J.Read, D.C.Richardson, J.S.Richardson, T.C.Terwilliger. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annu. Rev. Biophys. 42, 265-287 (2013).


 244M.Kyoung, Y.Zhang, J.Diao, S.Chu, A.T.Brunger. Studying calcium-triggered vesicle fusion in a single vesicle-vesicle content and lipid-mixing system. Nature Protocols 8, 1-16 (2013).
 243J.Diao, P.Grob, D.J.Cipriano, M.Kyoung, Y.Zhang, S.Shah, A.Nguyen, M.Padolina, A.Srivastava, M.Vrljic, A.Shah, E.Nogales, S.Chu, A.T.Brunger. Synaptic proteins promote calcium-triggered fusion from point contract to full fusion. eLife 1, e00109 (2012).
 242A.T.Brunger, P.D.Adams, P.Fromme, R.Fromme, M.Levitt, G.F. Schroder. Improving the accuracy of macromolecular structure refinement at 7 A resolution. Structure 20, 957-966 (2012).
 241T.C.Terwilliger, R.J.Read, P.D.Adams, A.T.Brunger, P.V.Afonine, R.W.Grosse-Kunstleve, L.W. Hung. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement, Acta Crystallogr. D68, 861-870 (2012).
 240A.Fischer, S.Sambashivan, A.T.Brunger, M.Montal. Beltless translocation domain of botulinum neurotoxin A embodies a minimum ion-conductive channel. J.Biol.Chem.287, 1657-1661 (2012).
 239A.T.Brunger, P.D.Adams. Refinement of X-ray crystal structures. In: Comprehensive Biophysics, Vol 1., E. Egelman, Ed., Elsevier, pp. 105-115 (2012).
 238A.T.Brunger, D.Das, A.M.Deacon, J.Grant,T.C.Terwilliger, R.J.Read, P.D.Adams, M.Levitt, G.F.Schroeder. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Cryst. D68, 391-403 (2012).
 237D.Arac, A.A.Boucard, M.F.Bolliger, J.Nguyen, S.M.Soltis, T.C.Sudhof, A.T.Brunger. A novel evolutionarily conserved domain of cell-adhesion GPCRs mediates autoproteolysis. EMBO J. 31, 1364-1378 (2012).
 236D.J.O’Donovan, I.Stokes-Rees, Y.Nam, S.C.Blacklow, G.F.Schroeder, A.T. Brunger, P.Sliz. A grid-enabled web service for low-resolution crystal structure refinement. Acta Cryst D68, 261-267 (2012).


 235M. Vrljic, P. Strop, R.C. Hill, K.C. Hansen, S. Chu, A.T. Brunger. Post-translational modifications and lipid binding profile of insect cell-expressed full-length mammalian synaptotagmin 1. Biochemistry 50, 9998-10012 (2011).
 234R.J.Read, P.D.Adams, W.B.Arendall III, A.T.Brunger, P.Emsley, R.P.Joosten, G.J. Kleywegt, E.B.Krissinel, T.Lütteke, Z.Otwinowski, A.Perrakis, J.S.Richardson, W.H.Sheffler, J.L.Smith, I.J.Tickle, G.Vriend, P.H.Zwart, A new generation of crystallographic validation tools for the Protein Data Bank, Structure 19, 1395-1412 (2011)
 233M.Kyoung, A.Srivastava, Y.Zhang, J.Diao, M.Vrljic, P.Grob, E. Nogales, S.Chu, A.T.Brunger, In vitro system capable of differentiating fast calcium- triggered content mixing from lipid exchange for mechanistic studies of neurotransmitter release. Proc. Natl. Acad. Sci. USA 108, E304-E313 (2011)
 232T.D.Fenn, M.J.Schnieders, M.Mustyakimov, P.Langan, V.S.Pande, A.T.Brunger, Reintroducing electrostatics into macromolecular crystallographic refinement: Application to neutron crystallography and DNA hydration, Structure 19, 523-533 (2011).


 231A.T. Brunger, P. Strop, M. Vrljic, S. Chu, K.R. Weninger, Three-dimensional molecular modeling with single molecule FRET, J. Struct. Biol.173, 497-505 (2011).
 230G.F.Schroeder, M.Levitt, A.T.Brunger, Super-resolution biomolecular crystallography with low-resolution data. Nature 464, 1218-1222 (2010).
 229M. Vrljic, P.Strop, J.A.Ernst, R.B.Sutton, S.Chu, A.T.Brunger, Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+-triggered vesicle fusion. Nat. Struct. Mol. Biol.17, 325-331 (2010).
 228U.B.Choi, P. Strop, M.Vrljic, S.Chu, A.T.Brunger, K.Weninger, Single molecule FRET-derived model of the synaptogagmin 1 - SNARE fusion complex. Nat. Struct. Mol. Biol.17, 318-324 (2010).
 227J.E.Zuniga,J.T.Hammill,O.Drory,J.E.Nuss,J.C.Burnett,R.Gussio,P.Wipf,S.Bavari,A.T.Brunger, Iterative structure-based peptide-like inhibitor design against the botulinum neurotoxin serotype A. PLoS one 5 e11378 (2010).
 226S.Vivona,C.W.Liu,P.Strop,V.Rossi,F.Filippini,A.T.Brunger, The longin SNARE VAMP7/TI-VAMP adopts a closed conformation. J. Biol. Chem 285, 17965-17973 (2010).
 225T.D.Fenn, M.J.Schnieders,A.T.Brunger, A smooth and differentiable bulk-solvent model for macromolecular diffraction. Acta Cryst.D66, 1024-1031 (2010).
 224C. Zhang, D. Atasoy, D. Arac, X. Yang, M.V. Fucillo, A.J. Robison, J. Ko, A.T.Brunger, T.C.Sudhof. Neurexin physically and functionally interacts with GABAA receptors. Neuron 66, 403-416 (2010).
 223T.D.Fenn, M.J.Schnieders, A.T.Brunger, V.S.Pande, Polarizable atomic multipole X-ray refinement: hydration geometry and application to macromolecules. Biophys J. 98, 2984-2992 (2010).


 222A.T. Brunger and J.A. Wells, Obituary: Warren L. DeLano 21 June 1972 - 3 November 2009, Nat. Struct. Mol. Biol. 16, 1202-1203 (2009).
 221J.Ko, C. Zhang, D. Arac, A.A. Boucard, A.T. Brunger, T.C. Sudhof, Neuroligin-1 performs neurexin-dependent and neurexin-independent functions in synapse validation. Embo J.28, 3244-3255 (2009)
 220A.T.Brunger, A.Rummel, Receptor and substrate interactions of clostridial neurotoxins. Toxicon 54, 550-560 (2009).
 219M.J.Schnieders,T.D.Fenn,V.S.Pande, A.T.Brunger, Polarizable atomic multipole X-ray refinement: application to peptide crystals. Acta Cryst. D65, 952-965 (2009).
 218A.T. Brunger, K. Weninger, M. Bowen, S Chu, Single-molecule studies of the neuronal SNARE fusion machinery. Ann. Rev. Biochem.78, 903-928 (2009).
 217W. Li, D. Tu, L. Li, R. Ghirlando, A.T. Brunger, Y. Ye, Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2ge. Proc. Natl. Acad. Sci. USA 106, 3722-3727 (2009).
 216A.T. Brunger, B. DeLaBarre, J.M. Davies, and W.I. Weis. X-ray structure determination at low resolution. Acta Cryst D56, 128-133 (2009).


 215J.E. Zuniga, J.J. Schmidt, T. Fenn, J.C. Burnett, D, Arac, R. Gussio, R.G. Stafford, S,S. Badie, S. Bavari, and A.T. Brunger, A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate. Structure 16, 1588-1597 (2008).
 214J.M.Davies, A.T.Brunger, W.I.Weis, Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change. Structure 16, 715-726, 2008.
 213A.T.Brunger, R.Jin, M.A.Breidenbach, Highly specific interactions between botulinum neurotoxins and synaptic vesicle proteins. Cell.Mol.Life Sci. 65, 2296-2306 (2008)
 212K.Weninger, M.E.Bowen, U.B.Choi, S.Chu, and A.T.Brunger, Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex. Structure 16, 308-320 (2008).
 211A.Schweizer Burguete, T.D.Fenn, A.T.Brunger, and S.R.Pfeffer, Rab and Arl GTPase family members cooperate in the localization of the Golgin GCC185. Cell 132, 286-298 (2008).
 210P.Strop, S.E.Kaiser, M.Vrljic, and A.T.Brunger. The structure of the yeast plasma membrane SNARE complex reveals destabilizing water filled cavities. J. Biol. Chem, 283, 1113-1119 (2008).


 209D.Arac, A.A.Boucard, E.Ozkan, P.Strop, E.Newell, T.C.Sudhof, A.T.Brunger. Structures of Neuroligin-1 and the Neuroligin-1/Neurexin-1b complex reveal specific protein-protein and protein-Ca2+ interactions. Neuron 56, 992-1003 (2007).
 208D.M.Pinkas, P.Strop, A.T.Brunger, C.Koshla, Transglutaminase 2 undergoes a large conformational change upon activation. PLOS Biology 5 2788-2796 (2007).
 207G.F.Schroder, A.T. Brunger, M. Levitt. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 15, 1630-1641 (2007).
 206A.T. Brunger, Version 1.2 of the Crystallography and NMR System. Nature Protocols 2, 2728-2733 (2007).
 205A.T. Brunger, M.A. Breidenbach, R. Jin, A. Fischer, J.S. Santos, M. Montal. Botulinum neurotoxin heavy chain belt as an intramolecular chaperone for the light chain, PLOS Pathogens 3, 1191-1194 (2007).
 204D. Tu, W. Li, Y. Ye, A.T. Brunger. Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p. Proc. Natl. Acad. Sci. USA 104, 15599=15606
 203R. Jin, S. Sikorra, C.M. Stegmann,A. Pich, T. Binz, and A.T. Brunger, Structural and biochemical studies of botulinum neurotoxin serotype C1 light chain protease: Implications for dual substrate specificity, Biochemistry 46, 10685-10693 (2007)
 202B.J.C Janssen, R.J. Read, A.T. Brunger, P. Gros, Crystallographic evidence for deviating C3b structure? Nature 448, doi:10.1038/nature06102 (2007).
 201M.J. Anderson, B. DeLaBarre, A. Raghunathan, B.O. Palsson, A.T.Brunger, and S.R. Quake, Crystal structure of a hyperactive Escherchia coli glycerol kinase mutant Gly230Asp obtained using microfluidic crystallization devices, Biochemistry 46, 5722-5731 (2007).
 200W. Li, D. Tu,A.T. Brunger, and Y. Ye, A ubiquitin ligase transfers preformed polyubiquitin chains from a conjugate enzyme to a substrate, Nature 446, 333-337 (2007).
 199J.C. Burnett, G. Ruthel, C.M. Stegmann, R.G. Panchal, T.L. Nguyen, A.R. Hermone, R.G. Stafford, D.J. Lane, T.A. Kenny, C.F. McGrath, P.Wipf, A.M. Stahl, J.J. Schmidt, R.Gussio, A.T. Brunger, and S. Bavari, Inhibition of metalloprotease botulinum serotype A from a pseudo-peptide binding mode to a small molecule that is active in primary neurons, J. Biol. Chem. 282, 5004-5014 (2007).
 198P. Strop, M.R. Brzustowicz, and A.T. Brunger, Ab initio molecular-replacement phasing for symmetric helical membrane proteins. Acta Cryst. D 63, 188-196 (2007).


 197R. Jin, A. Rummel, T. Binz, and A.T. Brunger, Botulinum neurotoxin B recognizes its protein receptor with high affinity and specificity, Nature 444, 1092-1095 (2006).
 196P.M. Kasson, N.W. Kelley, N. Singhal, M. Vrljic, A.T. Brunger, and V.S. Pande, Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion, Proc. Natl Acad. Sci USA 103, 11916-11921 (2006).
 195J.G. Zalatan, T.D. Fenn, A.T. Brunger, and D. Herschlag, Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: Implications for mechanism and evolution, Biochemistry, 45, 9788-9803 (2006).
 194B. DeLaBarre and A.T. Brunger, Considerations for the refinement of low resolution crystal structures, Acta Crystallographica D 26, 923-932 (2006).
 193B. DeLaBarre, J.C. Christianson, R.R. Kopito, A.T. Brunger, Central pore residues mediate the p97/VCP activity required for ERAD. Molecular Cell 22, 451-462 (2006).
 192M. Bowen and A.T. Brunger, Conformation of the synaptobrevin transmembrane domain Proc. Natl. Acad. Sci. USA 103, 8378-8383 (2006)
 191A.T. Brunger and B. DeLaBarre, Structure and mechanism of the ATPase VCP/P97: computational challenge for structure determination at low resolution. In: Modelling molecular structure and reactivity in biological systems, K.J. Naidoo, J. Brady, M.J. Field, J. Gao, M. Hann, Eds., Royal Society of Chemistry Publishing (2006), pp. 58-65.
 190A.T. Brunger, Structure and function of SNARE and SNARE-interacting proteins. Quarterly Reviews of Biophysics 38, 1-47 (2006)
 189S.M. Dennison, M.E. Bowen, A.T. Brunger, and B.R. Lentz, Neuronal SNAREs do not trigger fusion between synthetic membranes but do promote PEG-mediated membrane fusion, Biophysical Journal 90, 1661-1675 (2006).


 188P.M. Kasson, J.B. Huppa, M.M. Davis, and A.T. Brunger, A hybrid machine-learning approach for segmentation of protein localization data, Bioinformatics 21, 3778-3786 (2005).
 187J. Aishima, D.S. Russel, L.J. .Guibas, P.D. Adams, and A.T. Brunger , Automated crystallographic ligand building using the medial axis transform of an electron density isosurface, Acta Cryst. D 61, 1354-1363 (2005).
 186P. Strop and A.T. Brunger, Refractive index based determination of detergent concentration and its application to the study of membrane proteins, Protein Science 14, 2207-2211 (2005).
 185S.E. Kaiser, J.H. Brickner, A.R. Reilein, T.D. Fenn, P. Walter, and A.T. Brunger, Structural basis of FFAT motif-mediated ER targeting, Structure 13, 1035-1045 (2005).
 184M.A. Breidenbach and A.T Brunger, New insights into clostridial neurotoxin-SNARE interactions, Trends in Molecular Medicine 11, 378-381 (2005).
 183R. Jin, J.R. Junutula, H.T. Matern, K.E. Ervin, R.H. Scheller, and A.T. Brunger, Exo84 and Sec5 are competitive regulatory Sec6/8 effectors to the RalA GTPase, EMBO J. 24, 2064-2074 (2005).
 182M.A. Breidenbach and A. T. Brunger, 2.3 Ă crystal structure of tetanus neurotoxin light chain, Biochemistry 44, 7450-7457 (2005).
 181M.E. Bowen, K. Weninger, J. Ernst, S. Chu, and A.T. Brunger, Single molecule studies of synaptotagmin and complexin binding to the SNARE complex, Biophys. J. 89, 690-702 (2005).
 180B.DeLaBarre and A.T. Brunger, Nucleotide dependent motion and mechanism of action of p97/VCP, J. Mol. Biol. 347, 437-452 (2005).
 179A. T. Brunger, Low-resolution crystallography is coming of age. Structure 13, 171-172 (2005)
 178M. R. Brzustowicz and A. T. Brunger, X-ray scattering from unilamellar lipid vesicles, J. Appl. Cryst. 38, 126-131 (2005).
 177P. Kasson, J. Huppa, M. Krogsgaard, M. Davis, and A.T. Brunger, Quantitative Imaging of Lymphocyte Membrane Protein Reorganization and Signaling, Biophys. J. 88, 579-589 (2005).


 176M.A.Breidenbach, A.T.Brunger, Substrate recognition strategy for botulinum neurotoxin serotype A, Nature 432 925-929 (2004).
 175M.E. Bowen, K. Weninger, A.T. Brunger , and S. Chu, Single molecule observation of liposome - bilayer fusion thermally induced by SNAREs, Biophys. J. 87, 3569-3584 (2004)
 174P. Strop, A. J. Bankovich, K. C. Hansen, K. C. Garcia and A. T. Brunger, Structure of a Human A-type Potassium Channel Interacting Protein DPPX, a Member of the Dipeptidyl Aminopeptidase Family, J. Mol. Biol. 343, 1055-1065 (2004)
 173C. Chaudhry, A.L. Horwich, A.T. Brunger, and P. D. Adams, Exploring the structural dynamics of the E. Coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states, J. Mol. Biol. 342, 229-245(2004)


 172C. M. Weeks, P. D. Adams, J. Berendzen, A. T. Brunger, E. J. Dodson, R.W. Grosse-Kunstleve, T. R. Schneider, G. M., Sheldrick, T. C. Terwilliger, M. Turkenburg, and I. UsĂłn, Automatic Solution of Heavy-Atom Substructures, Methods in Enzymology 374, 37-83 (2003).
 171K. Weninger, M.E. Bowen, S. Chu, and A.T. Brunger, Single molecule studies of SNARE complex assembly reveal parallel and anti-parallel configurations, Proceedings of the National Academy of Sciences USA100, 14800-14805 (2003).
 170A.T. Brunger and B.DeLaBarre, NSF and p97/VCP: Similar at First, Different at Last, FEBS Letters 555, 126-133(2003).
 169C. Chaudhry, G. W. Farr, M. J. Todd, H. S. Rye, A. T. Brunger, P. D. Adams, A. L. Horwich, and P. B. Sigler, Role of the gamma-phosphate of ATP in triggering protein folding by GroEL–GroES: function, structure and energetics. EMBO Journal 22, 4877-4887.
 168M.A. Wilson and A.T. Brunger, Domain flexibility in the 1.75 Ă… resolution crystal structure of Pb2+-calmodulin, Acta Cryst.D59, 1782-1792 (2003).
 167J. Furst, R.B. Sutton, J. Chen, A.T. Brunger, and N. Grigorieff, Electron cryo-microscopy Structure of N-ethyl Maleimide Sensitive Factor at 11 Ă… Resolution, EMBO Journal 22, 4365-4374 (2003).
 166B. DeLaBarre and A.T. Brunger, Complete Structure of p97/Valosin-Containing Protein Reveals Communication Between Nucleotide Domains, Nature Structural Biology 10, 856-863 (2003).
 165S. Fukai, H.T. Matern, J.R. Jagath, R.H. Scheller, and A.T. Brunger, Structural basis of the interaction between RalA and Sec5, a subunit of the Sec6/8 complex, EMBO Journal 22, 3267-3278 (2003).
 164P.D. Adams, R.W. Grosse-Kunstleve and A.T. Brunger, Methods Biochem. Anal. 44, 75-87 (2003).
 163J.A. Ernst and A.T. Brunger , High resolution structure, stability, and synaptotagmin binding of a truncated neuronal SNARE complex, J. Biol. Chem. 278 , 8630-8636 (2003)


 162M.E. Bowen, D.M. Engelman, A.T. Brunger , Mutational Analysis of Synaptobrevin Transmembrane Domain Oliogmerization, Biochemistry 41 , 15861-15866 (2002)
 161I. Rouiller, B. DeLaBarre, A.P. May, W. I. Weis, A.T. Brunger, R.A. Milligan, and E.M. Wilson-Kubalek, Conformational Changes of the Multifunction p97 AAA ATPase during its ATPase Cycle, Nature Structural Biology, 9 , 950-957(2002).
 160K.E. Gottschalk, P.D. Adams, A.T. Brunger , and H. Kessler, Transmembrane signal transduction of the IIbĂź3 integrin Protein Science 11 , 1800-1812 (2002).
 159 A.T. Brunger and P.D. Adams, Molecular dynamics applied to X-ray structure refinement, Accounts of Chemical Research 35 , 404-412 (2002).
 158P. De Camilli, H. Chen, J. Hyman, E. Panepucci, A. Bateman, and A.T. Brunger, The ENTH domain, FEBS Letters, 25686, 11-18 (2002).
 157H.R. Saibil, and A.T. Brunger, Macromolecular assemblages Machines and networks, Editorial overview. Current Opinion in Structural Biology 12, 215-216 (2002).


 156G.A. Tavares, E.H. Panepucci, and A.T. Brunger, Structural Characterization of the Intramolecular Interaction between the SH3 and Guanylate Kinase Domains of PSD-95 Molecular Cell, Vol 8, 1313-1325 (2001).
 155 A. T. Brunger , P. D. Adams, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J.-S. Jiang, N. S. Pannu, R. J. Read, L. M. Rice & T. Simonson, The structure determination language of the Crystallography & NMR System. In: International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules. Dordrecht: Kluwer Academic Publishers, The Netherlands. pp. 710-716 (2001).
 154 A. T. Brunger , P. D. Adams & L. M. Rice, Enhanced macromolecular refinement by simulated annealing. In: International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules. Dordrecht: Kluwer Academic Publishers, The Netherlands. pp. 375-381 (2001)
 153A.T. Brunger, Structural insights into the molecular mechanism of calcium-dependent vesicle-membrane fusion. Current Opinion in Structural Biology 11, 163-173 (2001).
 152 A. T. Brunger , Structure of proteins involved in synaptic vesicle fusion in neurons. Ann. Rev. Biophys. Biomol. Struct. 30 , 157-171 (2001).
 151F. X. Zhou, H.J. Merianos, A.T. Brunger , and D. M. Engelman, Polar residues drive association of polyleucine transmembrane helices. Proc. Natl. Acad. Sci. USA 98 , 2250-2255 (2001).


 150M.A. Willis, B. Bishop, L. Regan, and A.T. Brunger , Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core. Structure, Folding, and Design 8 , 1319-1328 (2000).
 149C. Stroupe and A.T. Brunger, Crystal structures of a Rab protein in its inactive and active conformations, Journal Molecular Biology 304, 585-598 (2000).
 148L.M. Rice, T.N. Earnest, and A.T. Brunger, Single wavelength anomalous diffraction phasing revisited. Acta Cryst. D56, 1413-1420 (2000).
 147A.T. Brunger and E.D. Laue, New approaches to study macromolecular structure and function. Editorial Overview. Current Opinion in Structural Biology 10:557 (2000).
 146M.A. Wilson and A.T. Brunger, The 1.0 Ă… crystal structure of Ca2+ bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. J. Mol. Biol. 301, 1237-1256 (2000).
 145A.T. Brunger, Structural insights into the molecular mechanism of Ca2+-dependent exocytosis. Current Opinion in Neurobiology 10, 293-302 (2000).
 144J. Hyman, H. Chen, P. DeCamilli, P.P. DiFiore and A.T. Brunger, Epsin1 undergoes nucleocytosolic shuttling and its ENTH domain, structurally similar to Armadillo and HEAT repeats, interacts with the transcription factor PLZF, Journal Cell Biology 149, 537-545 (2000).
 143F. X. Zhou, M. J. Cocco, W. P. Russ, A. T. Brunger, and D. M. Engelman, Interhelical hydrogen bonding is a danger and an opportunity in membrane proteins. Nature Structural Biology 7, 154-159 (2000).


 142N. Ota, C. Stroupe, J.M.S. Ferreira-da-Silva, S.A. Shah, M. Mares-Guia, and A. T. Brunger, Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine, Proteins: Structure, Function, and Genetics 37, 641-653 (1999).
 141R. B. Sutton, J. A. Ernst, and A. T. Brunger, Crystal structure of the cytosolic C2A-C2B domains of synaptotagmin III: implications for Ca 2+ -independent SNARE complex interaction, J. Cell Biol. 147, 589-598 (1999).
 140A. T. Brunger, P. D. Adams, L. M. Rice, Annealing in crystallography: a powerful optimization tool, Progress in Biophysics & Molecular Biology 72, 135-155 (1999).
 139L. M. Rice and A. T. Brunger, Crystal structure of the vesicular transport protein Sec17: implications for SNAP function in SNARE complex disassembly, Molecular Cell 4, 85-95 (1999).
 138R. C. Yu, R. Jahn, and A. T. Brunger, NSF N-terminal domain crystal structure: models of NSF function, Molecular Cell 4, 97-107 (1999).
 137R. W. Grosse-Kunstleve and A. T. Brunger, A highly automated heavy-atom search procedure for macromolecular structures. Acta Cryst. D55, 1568-1577 (1999).
 136A. Kukol, P. D. Adams, L. M. Rice, A. T. Brunger, and I. T. Arkin, Experimentally based orientational refinement of membrane protein models: a structure for the Influenza A M2 H+ channel. J. Mol. Biol. 286, 951-962 (1999)
 135Y. Karimi-Nejad, F. A. A. Mulder, J. R. Martin, A. T. Brunger, D. Schipper and R. Boelens, NMR studies of the 269 residue serine protease PB92 from Bacillus alcalophilus. NMR in Supramolecular Chemistry, M. Pons, ed., 227-246, Kluwer Academic Publishers (1999).
 134I. T. Arkin and A. T. Brunger, Statistical analysis of predicted transmembrane a-helices. Biochimica et Biophysica Acta 1429, 113-128 (1999).
 133T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kale, J. A. Board, Jr., J. Hermans, and K. Schulten, Algorithmic challenges in computational molecular biophysics. Journal of Computational Physics 150, 1-40 (1999).
 131K. M. Fiebig, L. M. Rice, E. Pollock, and A. T. Brunger. Folding intermediates of SNARE complex assembly. Nature Structural Biology 6, 117-123 (1999).
 130C. Ostermeier and A. T. Brunger, Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A, Cell 96, 363-374 (1999).
 129T. R. Schneider, A. T. Brunger, and M. Nilges. Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory. J. Mol. Biol. 285, 727-740 (1999).
 128S. A. Shah and A. T. Brunger, The 1.8 Ă… crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure. J. Mol. Biol. 285, 1577-1587 (1999).
 127P. D. Adams, N. S. Pannu, R. J. Read, and A. T. Brunger, Extending the limits of molecular replacement through combined simulated annealing and maximum likelihood refinement. Acta Cryst. D, 55, 181-190 (1999).


 132Y. Karimi-Nejad, G. L. Warren, D. Schipper, A. T. Brunger, and R. Boelens, NMR Structure calculation methods for large proteins. Application of torsion angle dynamics and distance geometry / simulated annealing to the 269-residue protein serine protease PB92. Mol. Phys. 95, 1099-1112 (1998).
 126D. Fasshauer, R. B. Sutton, A. T. Brunger, and R. Jahn. Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q- and R-SNAREs. Proceedings of the National Academy of Sciences, U. S. A. 95, 15781-15786 (1998).
 125L. M. Rice, P. D. Adams, Y. Shamoo, and A. T. Brunger, Phase improvement by multi-start simulated annealing refinement and structure factor averaging, J. Appl. Crystallography 31, 798-805 (1998).
 124A. DiNola and A. T. Brunger, Free energy calculations in globular proteins: methods to reduce errors. J. Comp. Chem. 19, 1229-1240 (1998).
 123P. D. Adams, A. S. Lee, A. T. Brunger, and D. M. Engelman, Models for the transmembrane region of the phospholamban pentamer: which is correct? Ann. New York Academy of Sciences 853, 178-185 (1998).
 122A. T. Brunger, P. D. Adams, and L. M. Rice. Recent developments for the efficient crystallographic refinement of macromolecular structures. Current Opinion in Structural Biology 8, 606-611 (1998).
 121R.B.Sutton, D.Fasshauer, R.Jahn, A.T.Brunger. Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 A resolution. Nature 395, 347-353 (1998).
 120R. C. Yu, P. I. Hanson, R. Jahn, and A. T. Brunger, Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP, Nature Structural Biology 5, 803-811 (1998).
 119A.T.Brunger, P. D.Adams, G. M.Clore, W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren, Crystallography & NMR system (CNS): A new software system for macromolecular structure determination, Acta Cryst. D 54, 905-921 (1998).
 118D. Fasshauer, W. K. Eliason, A. T. Brunger, and R. Jahn, Identification of a minimal core of the synaptic SNARE-complex sufficient for reversible assembly and disassembly. Biochemistry 37, 10345-10353 (1998).
 117K. G. Fleming, T. M. Hohl, R. C. Yu, S. A. MĂĽller, B. Wolpensinger, A. Engel, H. Engelhardt, A. T. Brunger, T. H. Söllner, P. I. Hanson, A revised model for the oligomeric state of the N-ethylmaleimide sensitive factor, NSF, J. Biol. Chemistry 273, 15675-15681 (1998).
 116D. L. Daniels, A. R. Cohen, J. M. Anderson, and A. T. Brunger, Structural basis of class II PDZ domain target recognition: crystal structure of the hCASK PDZ domain, Nature Structural Biology 5, 317-324 (1998).
 115A. T. Brunger, P. D. Adams, and L. M. Rice. New applications of simulated annealing in crystallographic refinement. In: Direct Methods for Solving Macromolecular Structures, S. Fortier, Ed., Kluwer, 143-157 (1998).
 114I. T. Arkin, S. I. Sukharev, P. Blount, C. Kung, A. T. Brunger, Helicity, membrane incorporation, orientation and thermal stability of the large conductance mechanosensitive ion channel from E. coli, Biochimica et Biophysica Acta 1369, 131-140 (1998).


 113N. Ota and A. T. Brunger, Overcoming barriers in macromolecular simulations: Non-Boltzmann thermodynamic integration. Theoretical Chemistry Accounts 98, 171-181 (1997).
 112A. T. Brunger, X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997).
 111D. Fasshauer, H. Otto, W. K. Eliason, R. Jahn, and A. T. Brunger, Structural changes are associated with soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor complex formation, J. Biol. Chem. 272, 28036-28041 (1997).
 110I. T. Arkin, K. R. MacKenzie, and A. T. Brunger, Site-directed dichroism is a method for obtaining rotational and orientational constraints for oriented polymers, Journal of the American Chemical Society 119, 8973-8980 (1997).
 109L. M. Rice, P. Brennwald, and A. T. Brunger, Formation of a yeast SNARE complex is accompanied by significant structural changes, FEBS Lett. 415, 49-55 (1997).
 108S. A. Shah, B. W. Shen, and A. T. Brunger, Human ornithine aminotransferase complexed with L-canaline and gabaculine: structural basis for substrate recognition, Structure 5, 1067-1075 (1997).
 107I. T. Arkin, A. T. Brunger, and D. M. Engelman, Are there dominant membrane protein families with a given number of helices?, Proteins: Structure, Function, and Genetics 28, 465-466 (1997).
 106T. Simonson, C. F. Wong, and A. T. Brunger, Classical and quantum simulations of tryptophan in solution, Journal of Physical Chemistry, J. Phys. Chem. A 101, 1935-1945 (1997).
 105G. Rossi, A. Salminen, L. M. Rice, A. T. Brunger, and P. Brennwald, Analysis of a yeast SNARE complex reveals remarkable similarity to the neuronal SNARE complex and a novel function for the C-terminus of the SNAP-25 homolog, Sec9, J. Biol. Chem. 272 16610-16617 (1997).
 104I. T. Arkin, P. D. Adams, A. T. Brunger, S. O. Smith, D. M. Engelman, Structural perspectives of phospholamban, a helical transmembrane pentamer, Annual Review of Biophysics and Biomolecular Structure 26, 157-179 (1997).
 103I. T. Arkin, P. D. Adams, S. Aimoto, D. M. Engelman, S. O. Smith, Structure of the transmembrane cysteine residues in the phospholamban ion channel, J. Membrane Biol. 155, 199-206 (1997).
 102A. T. Brunger, Free R value: Cross-validation in crystallography, Methods in Enzym. 277, 366-396 (1997).
 101A. T. Brunger and L. M. Rice, Crystallographic refinement by simulated annealing: methods and applications, Methods in Enzym. 277, 243-269 (1997).
 100P. D. Adams, N. S. Pannu, R. J. Read, A. T. Brunger, Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement, Proc. Natl. Acad. Sci. USA 94, 5018-5023 (1997).
 99A. T. Brunger Patterson correlation searches and refinement, Methods in Enzym. 276, 558-580 (1997).
 98A. T. Brunger, P. D. Adams, L. M. Rice, New applications of simulated annealing in X-ray crystallography and solution NMR, Structure 15, 325-336 (1997).
 97D. Fasshauer, D. Bruns, B. Shen, R. Jahn and A. T. Brunger, A structural change occurs upon binding of syntaxin to SNAP-25, J. Biol. Chem. 272, 4582-4590 (1997).
 96E. G. Stein, L. M. Rice, A. T. Brunger, Torsion angle molecular dynamics: a new, efficient tool for NMR structure calculation, J. Magn. Reson. Ser. B 124, 154-164 (1997).


 95G. J. Kleywegt, A. T. Brunger, Checking your imagination: applications of the free R value, Structure 4, 897-904 (1996).
 94P. D. Adams, A. T. Brunger, Towards prediction of membrane protein structure, In Membrane Protein Assembly, G.v. Heijne, Ed., R. G.Landes Co., Austin, TX (1996).
 93P. D. Adams, D. M. Engelman, A. T. Brunger, An improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained by global searching, Proteins: Structure, Function, and Genetics 26, 257-261 (1996).
 92P. D. Adams, K. Braig, L. M. Rice, A. T. Brunger, Torsion angle dynamics refinement of the Chaperonin GroEL at 2.8 Å resolution, In: Macromolecular refinement, Proceedings of the CCP4 study weekend at Chester College, January 1996, E. Dodson, M. Moore, A. Ralph, S. Bailey, Eds., Council of the Central Laboratory of the Research Councils, 59-65 (1996).
 91A. T. Brunger, Recent Developments for Crystallographic refinement of macromolecules, Methods in Molecular Biology 56, 245-266 (1996).
 90A. M. J. J. Bonvin and A. T. Brunger, Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?, J. Biomol. NMR 7, 72-76 (1996).
 89G. Parkinson, J. Vojtechovsky, L. Clowney, A. T. Brunger, and H. M.Berman, New parameters for the refinement of nucleic acid containing structures, Acta Cryst. D 52, 57-64 (1996).
 88F. T. Burling, W. I. Weis, K. M. Flaherty, and A. T. Brunger, Direct observation of protein solvation and discrete disorder with experimental crystallographic phases, Science 271, 72-77 (1996).
 87P. F. Predki, V. Agrawal, A. T. Brunger, and L. Regan, How amino acid substitutions in a surface turn modulate protein stability, Nature Structural Biology 3, 54-58 (1996).


 86K. Braig, P. D. Adams, and A. T. Brunger, Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Ă… resolution, Nature Structural Biology 2, 1083-1094 (1995).
 85L. U. Roberts and A. T. Brunger, Phase improvement by cross-validated density modification, Acta Cryst. D 51, 990-1002 (1995).
 84W. L. DeLano and A. T. Brunger, The direct rotation function: rotational patterson correlation search applied to molecular replacement, Acta Cryst. D 51, 740-748 (1995).
 83A. T. Brunger and L. M. Rice, Simulated annealing applied to crystallographic structure refinement, In: Adaption of Simulated Annealing to Chemical Optimization Problems, J. H. Kalivas, Ed., Elsevier Science B. V., 259-280 (1995).
 82M. Engelman, B. Adair, A. T. Brunger, J. Hunt, T. Kahn, M. Lemmon, K. MacKenzie, and H. Treutlein, Helix-helix Interactions Inside Membranes. In: Biochemistry of Cell Membranes. A Compendium of Selected Topics, eds. Birkhaüser Verlag Basel/Switzerland (1995) pp. 297-310.
 81A. Hodel, L. M. Rice, T. Simonson, R. O. Fox, and A. T. Brunger, Proline cis/trans isomerization in staphylococcal nuclease: A multi-substate free energy perturbation study, Protein Science 4, 636-654 (1995).
 80A. M. J. J. Bonvin and A. T. Brunger, Conformational Variability of solution nuclear magnetic resonance structures, J. Mol. Biol. 250, 80-93 (1995).
 79P. D. Adams, I. T. Arkin, D. M. Engelman, A. T. Brunger, Computational searching and mutagenesis suggest a structure for phospholamban, a cardiac ion channel, Nature Structural Biology 2, 154-162 (1995).


 78D.-B. Huang, C.-H. Chang, C. Ainsworth, A. T. Brunger, M. Eulitz, A. Solomon, F. J. Stevens and M. Schiffer, Unusual domain pairing observed in a second high-resolution structure of a kappa-type immunoglobulin light-chain variable domain dimer, Biochemistry 33, 14848-14857 (1994).
 77I. T. Arkin, P. D. Adams, K. R. MacKenzie, M. A. Lemmon, A. T. Brunger, and D. M. Engelman, Structural organization of the pentameric transmembrane a-helices of phospholambin, a cardiac ion channel, EMBO Journal 13, 4757-4764 (1994).
 76W. L. DeLano and A. T. Brunger, Helix packing in proteins: prediction and energetic analysis of dimeric, trimeric, and tetrameric GCN4 coiled coil structures, Proteins: Structure, Function, and Genetics 20, 105-123 (1994).
 75J.-S. Jiang and A. T. Brunger, Protein hydration observed by x-ray diffraction: solvation properties of penicillopepsion and neuraminidase crystal structures, J. Mol. Biol. 243, 100-115 (1994).
 74L. M. Rice and A. T. Brunger, Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement, Proteins: Structure, Function, and Genetics 19, 277-290 (1994).
 73T. Simonson, A. T. Brunger, Solvation free energies estimated from macroscopic continuum theory: an accuracy assessment, J. Phys. Chem. 98, 4683-4694 (1994).
 72F. T. Burling, A. T. Brunger, Thermal motion and conformational disorder in protein crystal structures: Comparison of multi-conformer and time-averaging models, Israel Journal of Chemistry 34 165-175 (1994).
 71M. A. Lemmon, H. R. Treutlein, P. D. Adams, A. T. Brunger, D. M. Engelman, A Dimerization motif for transmembrane a-helices, Nature Structural Biology, 1, 157-163 (1994).


 70A. T. Brunger, Structure determination of antibodies and antibody-antigen complexes by molecular replacement, Immunomethods 3, Wilson, I. A., Ed., pp. 180-190, Academic Press (1993).
 69A. T. Brunger and M. Nilges, Computational challenges for three dimensional structure determination by X-ray crystallography and solution NMR spectroscopy, Quarterly Reviews of Biophysics 26, 49-125 (1993).
 68A. T. Brunger, G. M. Clore, A. M. Gronenborn, R. Saffrich, M. Nilges, Assessment of the Quality of Solution Nuclear Magnetic Resonance Structures by Complete Cross-Validation, Science 261, 328-331 (1993).
 67A. Hodel, T. Simonson, R. O. Fox, A. T. Brunger, Conformational Substates and Uncertainty in Macromolecular Free Energy Calculations, J. Phys. Chem. 97, 3409-3417 (1993).
 66A. T. Brunger, Assessment of phase accuracy by cross validation: The free R value. Methods and Applications, Acta Cryst. D 49, 24-36 (1993).
 62M. Nilges, A. T. Brunger, Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: Comparison to the X-ray structure, Proteins 15, 133-146 (1993).


 65A. T. Brunger, X-PLOR, version 3.1. A system for X-ray crystallography and NMR, Yale University Press, New Haven, CT (1992).
 64A. T. Brunger, Molecular replacement with X-PLOR: PC-refinement and free R value. In: Proceedings of the Daresbury Study Weekend on Molecular Replacement, Daresbury, United Kingdom (1992), 49-61.
 63H. R. Treutlein, M. A. Lemmon, D. M. Engelman, A. T. Brunger, The glycophorin A transmembrane domain dimer: Sequence-specific propensity for a right-handed coil of helices, Biochemistry 31, 12726-12733 (1992).
 61A. Hodel, S.-H. Kim, A. T. Brunger, Model bias in macromolecular crystal structures, Acta Cryst. A 48, 851-858 (1992).
 60T. Simonson, A. T. Brunger, Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations, Biochemistry 31, 8661-8674 (1992).
 59K. C. Garcia, P. M. Ronco, P. J. Verroust, A. T. Brunger, L. M. Amzel, Three dimensional structure of an angiotensin II-Fab complex at 3 Ă… resolution: hormone recognition by an anti-idiotypic antibody, Science 257, 502-507 (1992).
 58S. A. White, M. Nilges, A. Huang, A. T. Brunger, P. B. Moore, An NMR analysis of helix I from the 5S RNA of Escherichia coli, Biochemistry 31, 1610-1621 (1992).
 57A.T.Brunger, The free R value: a novel statistical quantity for assessing the accuracy of crystal structures, Nature 355, 472-474 (1992).
 56H. Treutlein, K. Schulten, M. Karplus A. T. Brunger, J. Deisenhofer, and H. Michel, Chromophore-protein interactions and the function of the photosynthetic reaction center: A molecular dynamics study, Proc. Natl. Acad. Sci. USA 89, 75-79 (1992).
 55J. Kuszewski, M. Nilges, A. T. Brunger, Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm, J. Biomolecular NMR 2, 33-56 (1992).


 54A. T. Brunger, A unified approach to crystallographic refinement and molecular replacement. In: Crystallographic Computing 5. From Chemistry to Biology, eds. D. Moras, A. D. Podjarny, J. C. Thierry, Oxford University Press, Oxford (1991), pp. 392-408.
 53M. Nilges, J. Kuszewski, A. T. Brunger, Sampling properties of simulated annealing and distance geometry. In: Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, ed. J. Hoch, Plenum Press, New York (1991), pp. 451-455.
 52J. Habazettl, M. Nilges, H. Oschkinat, A. T. Brunger, and T. A. Holak, NMR structures of proteins using stereospecific assignments and relaxation matrix refinement in a hybrid method of distance geometry and simulated annealing. In: Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, ed. J. Hoch, Plenum Press, New York (1991), pp. 395-408.
 51A. T. Brunger, Recent developments in crystallographic phasing and refinement of macromolecules, Current Opinion in Structural Biology 1, 1016-1022 (1991).
 50A. T. Brunger, Simulated annealing in crystallography, Ann. Rev. Phys. Chem. 42, 197-223 (1991).
 49A. T. Brunger, Refinement of three dimensional structures of proteins and nucleic acids. In: Topics in Molecular Biology, ed. J. M. Goodfellow, Macmillan Press Ltd, London (1991), pp. 137-178.
 48A. T. Brunger, M. Karplus, Molecular dynamics simulations with experimental restraints, Accounts Chemical Research 24, 54-61 (1991).
 47T. Simonson, D. Perahia, G. Bricogne, A. T. Brunger, Dielectric properties of proteins: microscopic and macroscopic theory, J. Chem. Phys. 88, 2701-2708 (1991).
 46A. T. Brunger, D. J. Leahy, T. R. Hynes, R. O. Fox, The 2.9 Ĺ resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten, J. Mol. Biol. 221, 239-256 (1991).
 45M. Nilges and A. T. Brunger, Automated modeling of coiled coils. Application to the GCN4 dimerization region, Protein Engineering 4, 649-659 (1991).
 44J. Kuriyan, K. Osapay, S. K. Burley, A. T. Brunger, M. Karplus, W. A. Hendrickson, Exploration of disorder in protein structures by X-ray restrained molecular dynamics, Proteins 10, 340-358 (1991).
 43M. Nilges, J. Habazettl, A. T. Brunger, T. A. Holak, Relaxation matrix refinement of the solution structure of squash trypsin inhibitor, J. Mol. Biol. 219, 499-510 (1991).
 42T. Simonson, D. Perahia, A. T. Brunger, Microscopic theory of the dielectric properties of proteins, Biophys. J. 59, 670-690 (1991).
 41A. T. Brunger, Solution of a Fab(26-10)/digoxin complex by generalized molecular replacement, Acta Cryst. A 47, 195-204 (1991).


 40A. T. Brunger, M. V. Milburn, L. Tong, A. M. de Vos, J. Jancarik, Z. Yamaizumi, S. Nishimura, E. Ohtsuka, S.-H. Kim. Crystal structure of an active form of ras protein, a complex of GTP analog and c-H-ras P21 catalytic domain, Proc. Natl. Acad. Sci. USA 87, 4849-4853 (1990).
 39A. T. Brunger, A. Krukowski, J. Erickson, Slow-cooling protocols for crystallographic refinement by simulated annealing, Acta Cryst. A 46, 585-593 (1990).
 38W. I. Weis, A. T. Brunger, J. J. Skehel, D. C. Wiley, Refinement of the influenza virus haemagglutinin by simulated annealing, J. Mol. Biol. 212, 737-761 (1990).
 37M. V. Milburn, L. Tong, A. M. de Vos, A. T. Brunger, Z. Yamaizumi, S. Nishimura, S.-H. Kim, Molecular Switch for Signal Transduction: Structural Differences Between Active and Inactive Forms of Protooncogenic ras Proteins, Science 247, 939-945 (1990).
 36A. T. Brunger, Extension of molecular replacement: A New search strategy based on Patterson correlation refinement, Acta Cryst. A 46, 46-57 (1990).
 35K. Haydock, C. Lim, A. T. Brunger, and M. Karplus. Simulation analysis of structures of the reaction pathway of RNase A, J. Am. Chem. Soc. 112, 3826-3831 (1990).


 34W. I. Weis and A. T. Brunger, Crystallographic refinement by simulated annealing. In: Proceedings of the Daresbury Study Weekend on Molecular Dynamics and Protein Refinement, Daresbury, United Kingdom, 16-28 (1989).
 33J. Kuriyan, A. T. Brunger, M. Karplus, W. A. Hendrickson, X-ray refinement of protein structures by simulated annealing: Test of the method on myohemerythrin, Acta Cryst. A 45, 396-409 (1989).
 32A. T. Brunger, A memory-efficient fast Fourier transformation algorithm for crystallographic refinement on supercomputers, Acta Cryst. A 45, 42-50 (1989).
 31A. T. Brunger, M. Karplus, G. A. Petsko, Crystallographic refinement by simulated annealing: Application to a 1.5 Ă… resolution structure of crambin, Acta Cryst. A 45, 50-61 (1989).


 30H. Treutlein, K. Schulten, J. Deisenhofer, H. Michel, A. T. Brunger, M. Karplus, Molecular dynamics simulation of the primary processes in the photosynthetic reaction center. In: The Photosynthetic Reaction Center: Structure and Dynamics, eds. J. Breton & A. Vermeglio, Plenum, New York (1988), pp. 139-150.
 29A. T. Brunger, Crystallographic refinement by simulated annealing. In: Crystallographic Computing 4: Techniques and New Technologies, eds. N. W. Isaacs and M. R. Taylor, Clarendon Press, Oxford (1988), pp. 126-140.
 28A. T. Brunger, Crystallographic refinement by simulated annealing: Application to a 2.8 Ĺ resolution structure of aspartate aminotransferase, J. Mol. Biol. 203, 803-816 (1988).
 27D. M. LeMaster, L. E. Kay, A. T. Brunger, J. H. Prestegard, Protein dynamics and distance determination by NOE measurements, FEBS Letters 236, 71-76 (1988).
 26A. T. Brunger, M. Karplus, Polar hydrogen positions in proteins: empirical energy function placement and neutron diffraction comparison, Proteins 4, 148-156 (1988).
 25L. X.-Q. Chen, R. A. Engh, A. T. Brunger, D. T. Nguyen, M. Karplus, G. R. Fleming, Dynamics simulation studies of apoazurin of Alcaligenes denitrificans, Biochemistry 27, 6908-6921 (1988).
 24G. M. Clore, M. Nilges, A. T. Brunger, A. M. Gronenborn, Determination of the backbone conformation of secretin by restrained molecular dynamics on the basis of interproton distance data, Eur. J. Biochem. 171, 479-484 (1988).
 23M. Nilges, A. M. Gronenborn, A. T. Brunger, G. M. Clore, Determination of three dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2, Protein Engineering 2, 27-38 (1988).


 22M. Karplus, A. T. Brunger, R. Elber, J. Kuriyan, Molecular dynamics: Applications to proteins". In: Structure & Expression Volume 1: From Proteins to Ribosomes, eds. R. H. Sarma & M. H. Sarma, Adenine Press (1987), pp. 55-65.
 21W. Nadler, A. T. Brunger, M. Karplus, K. Schulten, Molecular and stochastic dynamics of proteins, Proc. Natl.Acad. Sci. USA 84, 7933-7937 (1987).
 20A. T. Brunger, G. M. Clore, A. M. Gronenborn, M. Karplus, Solution conformations of human growth hormone releasing factor: Comparison of the restrained molecular dynamics and distance geometry methods for a system without long range distance data, Protein Engineering 1, 399-406 (1987).
 19A. T. Brunger, R. Huber, M. Karplus, Trypsinogen-trypsin transition: A molecular dynamics study of induced conformational change in the activation domain, Biochemistry 26, 5153-5162 (1987).
 18M. Nilges, G. M. Clore, A. M. Gronenborn, A. T. Brunger, L. Nilsson, The three dimensional solution structure of the DNA hexamer 5’d(CGATCG)2. Combined use of nuclear magnetic resonance and restrained molecular dynamics, Biochemistry 26, 3718-3733 (1987).
 17G. M. Clore, M. Nilges, A. T. Brunger, M. Karplus, A. M. Gronenborn, A comparison of the restrained molecular dynamics and distance geometry methods for determining three dimensional structures of proteins on the basis of interproton distances, FEBS Lett. 213, 269-277 (1987).
 16A.T.Brunger, J.Kuriyan, M.Karplus, Crystallographic R factor refinement by molecular dynamics, Science 235, 458-460 (1987).
 15A. T. Brunger, R. L. Campbell, G. M. Clore, A. M. Gronenborn, M. Karplus, G. A. Petsko, M. M. Teeter, Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints, Science 235, 1049-1053 (1987).


 14C. L. Brooks III, A. T. Brunger, C. Haydock, L. C. Allen, M. Karplus, Role of active site residues and solvation in RNase. In: International Symposium on Bioorganic Chemistry, Ann. N. Y. Acad. Sci. 471, 295-298 (1986).
 13G. M. Clore, M. Nilges, D. K. Sukumaran, A. T. Brunger, M. Karplus, A. M. Gronenborn, The three dimensional structure of a-purothionin in solution: Combined use of nuclear magnetic resonance, distance geometry, and restrained molecular dynamics, EMBO J. 5, 2729-2735 (1986).
 12G. M. Clore, A. T. Brunger, M. Karplus A. M. Gronenborn, Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: A model study of crambin, J. Mol. Biol. 191, 523-551 (1986).
 11A. T. Brunger, G. M. Clore, A. M. Gronenborn, M. Karplus, Three dimensional structure determination of proteins by molecular dynamics with interproton distance restraints: Application to crambin, Proc. Natl. Acad. Sci.USA 83, 3801-3805 (1986).
 10L. Nilsson, G. M. Clore, A. M. Gronenborn, A. T. Brunger, M. Karplus, Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: Application to 5'D(CGTACG)2, J. Mol. Biol. 188, 455-475 (1986).


 9A. T. Brunger, C. L. Brooks, M. Karplus, Molecular dynamics with stochastic boundaries. Application to the active site of proteins in solution. In: Molecular Dynamics and Protein Structure, Proceedings of a Workshop held 13-18 May 1984, University of North Carolina, ed. J. Hermans, University of North Carolina (1985), pp. 16-17.
 8A. T. Brunger, C. L. Brooks III, M. Karplus, Active site dynamics of ribonuclease A, Proc. Natl. Acad. Sci USA 82, 8458-8462 (1985).
 7G. M. Clore, A. M. Gronenborn, A. T. Brunger, M. Karplus, The solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia Coli: Combined use of 1H-nuclear magnetic resonance and restrained molecular dynamics, J. Mol. Biol. 186, 435-455 (1985).
 6C. L. Brooks III, A. T. Brunger, M. Karplus, Active site dynamics in protein molecules: A stochastic boundary molecular dynamics approach, Biopolymers 24 343-365 (1985).
 5A. T. Brunger, R. Peters, K. Schulten, Continuous fluorescence microphotolysis to observe lateral diffusion in membranes. Theoretical Methods and Applications, J. Chem. Phys. 82, 2147-2168 (1985).


 4A. T. Brunger, C. L. Brooks, M. Karplus, Stochastic boundary conditions for molecular dynamics simulations of ST2 water, Chem. Phys. Let. 105, 495-500 (1984).
 3A. T. Brunger, Z. Schulten, K. Schulten, A Network Thermodynamic investigation of stationary and non-stationary proton transport through proteins, Zeitschrift f. Phys. Chem. 136, 1-63 (1984).


 2K. Schulten, A. T. Brunger, W. Nadler, Z. Schulten, Generalized moment description of Brownian dynamics in biological systems. In: Synergetics - From Microscopic to Macroscopic Order, ed. E. Frehland, Springer, Berlin (1983), pp. 80-89.


 1R. Peters, A. T. Brunger, K. Schulten, Continuous fluorescence microphotolysis: A sensitive method for study of diffusion processes in single cells, Proc. Natl. Acad. Sci USA 78, 962-966 (1981).