ACS Publications. Most Trusted. Most Cited. Most Read
My Activity
CONTENT TYPES

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity

Cite this: Biochemistry 1995, 34, 27, 8576–8588
Publication Date (Print):July 11, 1995
https://doi.org/10.1021/bi00027a007
    ACS Legacy Archive

    Article Views

    884

    Altmetric

    -

    Citations

    LEARN ABOUT THESE METRICS
    Other access options

    Note: In lieu of an abstract, this is the article's first page.

    Free first page

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Cited By

    This article is cited by 156 publications.

    1. Jinan Wang, Yinglong Miao. Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket. Journal of Chemical Theory and Computation 2023, 19 (3) , 733-745. https://doi.org/10.1021/acs.jctc.2c01194
    2. Cécile Hilpert, Louis Beranger, Paulo C. T. Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli, Guillaume Launay. Facilitating CG Simulations with MAD: The MArtini Database Server. Journal of Chemical Information and Modeling 2023, 63 (3) , 702-710. https://doi.org/10.1021/acs.jcim.2c01375
    3. Oriol Gracia Carmona, Chris Oostenbrink. Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. Journal of Chemical Information and Modeling 2023, 63 (1) , 197-207. https://doi.org/10.1021/acs.jcim.2c01272
    4. Montgomery Gray, Paige E. Bowling, John M. Herbert. Systematic Evaluation of Counterpoise Correction in Density Functional Theory. Journal of Chemical Theory and Computation 2022, 18 (11) , 6742-6756. https://doi.org/10.1021/acs.jctc.2c00883
    5. Lara A. Patel, Phuong Chau, Serena Debesai, Leah Darwin, Chris Neale. Drug Discovery by Automated Adaptation of Chemical Structure and Identity. Journal of Chemical Theory and Computation 2022, 18 (8) , 5006-5024. https://doi.org/10.1021/acs.jctc.1c01271
    6. Miroslav Suruzhon, Michael S. Bodnarchuk, Antonella Ciancetta, Ian D. Wall, Jonathan W. Essex. Enhancing Ligand and Protein Sampling Using Sequential Monte Carlo. Journal of Chemical Theory and Computation 2022, 18 (6) , 3894-3910. https://doi.org/10.1021/acs.jctc.1c01198
    7. Maria M. Reif, Martin Zacharias. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications. Journal of Chemical Theory and Computation 2022, 18 (6) , 3873-3893. https://doi.org/10.1021/acs.jctc.1c01194
    8. Vilhelm Ekberg, Ulf Ryde. On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies. Journal of Chemical Theory and Computation 2021, 17 (8) , 5379-5391. https://doi.org/10.1021/acs.jctc.1c00374
    9. Sung Oh Woo, Myungkeun Oh, Lina Alhalhooly, Jasmin Farmakes, Arith J. Rajapakse, Zhongyu Yang, Philip G. Collins, Yongki Choi. Different Single-Enzyme Conformational Dynamics upon Binding Hydrolyzable or Nonhydrolyzable Ligands. The Journal of Physical Chemistry B 2021, 125 (22) , 5750-5756. https://doi.org/10.1021/acs.jpcb.1c01589
    10. Hugo Guterres, Sang-Jun Park, Wei Jiang, Wonpil Im. Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. Journal of Chemical Information and Modeling 2021, 61 (1) , 535-546. https://doi.org/10.1021/acs.jcim.0c01354
    11. Seonghoon Kim, Hiraku Oshima, Han Zhang, Nathan R. Kern, Suyong Re, Jumin Lee, Benoît Roux, Yuji Sugita, Wei Jiang, Wonpil Im. CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations. Journal of Chemical Theory and Computation 2020, 16 (11) , 7207-7218. https://doi.org/10.1021/acs.jctc.0c00884
    12. Timothy J. Giese, Darrin M. York. Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods. Journal of Chemical Theory and Computation 2019, 15 (10) , 5543-5562. https://doi.org/10.1021/acs.jctc.9b00401
    13. Wei Jiang, Christophe Chipot, Benoît Roux. Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD. Journal of Chemical Information and Modeling 2019, 59 (9) , 3794-3802. https://doi.org/10.1021/acs.jcim.9b00362
    14. Ai Niitsu, Suyong Re, Hiraku Oshima, Motoshi Kamiya, Yuji Sugita. De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations. Journal of Chemical Information and Modeling 2019, 59 (9) , 3879-3888. https://doi.org/10.1021/acs.jcim.9b00416
    15. Riccardo Capelli, Paolo Carloni, Michele Parrinello. Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics. The Journal of Physical Chemistry Letters 2019, 10 (12) , 3495-3499. https://doi.org/10.1021/acs.jpclett.9b01183
    16. Kalistyn H. Burley, Samuel C. Gill, Nathan M. Lim, David L. Mobley. Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo. Journal of Chemical Theory and Computation 2019, 15 (3) , 1848-1862. https://doi.org/10.1021/acs.jctc.8b01018
    17. João Marcelo Lamim Ribeiro, Pratyush Tiwary. Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE. Journal of Chemical Theory and Computation 2019, 15 (1) , 708-719. https://doi.org/10.1021/acs.jctc.8b00869
    18. Wei Jiang, Jonathan Thirman, Sunhwan Jo, Benoît Roux. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis. The Journal of Physical Chemistry B 2018, 122 (41) , 9435-9442. https://doi.org/10.1021/acs.jpcb.8b03277
    19. Junchao Xia, William Flynn, Ronald M. Levy. Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. Journal of Chemical Information and Modeling 2018, 58 (7) , 1356-1371. https://doi.org/10.1021/acs.jcim.8b00194
    20. Israel Cabeza de Vaca, Yue Qian, Jonah Z. Vilseck, Julian Tirado-Rives, William L. Jorgensen. Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding. Journal of Chemical Theory and Computation 2018, 14 (6) , 3279-3288. https://doi.org/10.1021/acs.jctc.8b00031
    21. Bing Xie, Trung Hai Nguyen, and David D. L. Minh . Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations. Journal of Chemical Theory and Computation 2017, 13 (6) , 2930-2944. https://doi.org/10.1021/acs.jctc.6b01183
    22. Xinqiang Ding, Jonah Z. Vilseck, Ryan L. Hayes, and Charles L. Brooks, III . Gibbs Sampler-Based λ-Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation. Journal of Chemical Theory and Computation 2017, 13 (6) , 2501-2510. https://doi.org/10.1021/acs.jctc.7b00204
    23. Hyelee Lee, Marcus Fischer, Brian K. Shoichet, and Shih-Yuan Liu . Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics. Journal of the American Chemical Society 2016, 138 (37) , 12021-12024. https://doi.org/10.1021/jacs.6b06566
    24. Nathan M. Lim, Lingle Wang, Robert Abel, and David L. Mobley . Sensitivity in Binding Free Energies Due to Protein Reorganization. Journal of Chemical Theory and Computation 2016, 12 (9) , 4620-4631. https://doi.org/10.1021/acs.jctc.6b00532
    25. Daniel J. Cole, Jonah Z. Vilseck, Julian Tirado-Rives, Mike C. Payne, and William L. Jorgensen . Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning. Journal of Chemical Theory and Computation 2016, 12 (5) , 2312-2323. https://doi.org/10.1021/acs.jctc.6b00027
    26. Mazen Ahmad, Volkhard Helms, Olga V. Kalinina, and Thomas Lengauer . The Role of Conformational Changes in Molecular Recognition. The Journal of Physical Chemistry B 2016, 120 (9) , 2138-2144. https://doi.org/10.1021/acs.jpcb.5b11593
    27. Thomas B. Steinbrecher, Markus Dahlgren, Daniel Cappel, Teng Lin, Lingle Wang, Goran Krilov, Robert Abel, Richard Friesner, and Woody Sherman . Accurate Binding Free Energy Predictions in Fragment Optimization. Journal of Chemical Information and Modeling 2015, 55 (11) , 2411-2420. https://doi.org/10.1021/acs.jcim.5b00538
    28. Yinglong Miao, Victoria A. Feher, and J. Andrew McCammon . Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. Journal of Chemical Theory and Computation 2015, 11 (8) , 3584-3595. https://doi.org/10.1021/acs.jctc.5b00436
    29. Sirish Kaushik Lakkaraju, E. Prabhu Raman, Wenbo Yu, and Alexander D. MacKerell, Jr. . Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2014, 10 (6) , 2281-2290. https://doi.org/10.1021/ct500201y
    30. Melek N. Ucisik, Zheng Zheng, John C. Faver, and Kenneth M. Merz . Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”. Journal of Chemical Theory and Computation 2014, 10 (3) , 1314-1325. https://doi.org/10.1021/ct400995c
    31. William J. Allen and Robert C. Rizzo . Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design. Journal of Chemical Information and Modeling 2014, 54 (2) , 518-529. https://doi.org/10.1021/ci400534h
    32. Matthew Merski and Brian K. Shoichet . The Impact of Introducing a Histidine into an Apolar Cavity Site on Docking and Ligand Recognition. Journal of Medicinal Chemistry 2013, 56 (7) , 2874-2884. https://doi.org/10.1021/jm301823g
    33. Mats Linder, Anirudh Ranganathan, and Tore Brinck . “Adapted Linear Interaction Energy”: A Structure-Based LIE Parametrization for Fast Prediction of Protein–Ligand Affinities. Journal of Chemical Theory and Computation 2013, 9 (2) , 1230-1239. https://doi.org/10.1021/ct300783e
    34. Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoı̂t Roux, and Wonpil Im . CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. Journal of Chemical Information and Modeling 2013, 53 (1) , 267-277. https://doi.org/10.1021/ci300505n
    35. E. Prabhu Raman, Kenno Vanommeslaeghe, and Alexander D. MacKerell, Jr. . Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. Journal of Chemical Theory and Computation 2012, 8 (10) , 3513-3525. https://doi.org/10.1021/ct300088r
    36. Enrico O. Purisima and Hervé Hogues . Protein–Ligand Binding Free Energies from Exhaustive Docking. The Journal of Physical Chemistry B 2012, 116 (23) , 6872-6879. https://doi.org/10.1021/jp212646s
    37. Jacob Poehlsgaard, Kasper Harpsøe, Flemming Steen Jørgensen, and Lars Olsen . A Robust Force Field Based Method for Calculating Conformational Energies of Charged Drug-Like Molecules. Journal of Chemical Information and Modeling 2012, 52 (2) , 409-419. https://doi.org/10.1021/ci200345f
    38. Seungil Han, Nicole Caspers, Richard P. Zaniewski, Brian M. Lacey, Andrew P. Tomaras, Xidong Feng, Kieran F. Geoghegan, and Veerabahu Shanmugasundaram . Distinctive Attributes of β-Lactam Target Proteins in Acinetobacter baumannii Relevant to Development of New Antibiotics. Journal of the American Chemical Society 2011, 133 (50) , 20536-20545. https://doi.org/10.1021/ja208835z
    39. Ilja V. Khavrutskii and Anders Wallqvist . Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. Journal of Chemical Theory and Computation 2011, 7 (9) , 3001-3011. https://doi.org/10.1021/ct2003786
    40. Robert D. Malmstrom and Stanley J. Watowich . Using Free Energy of Binding Calculations To Improve the Accuracy of Virtual Screening Predictions. Journal of Chemical Information and Modeling 2011, 51 (7) , 1648-1655. https://doi.org/10.1021/ci200126v
    41. Samuel Genheden, Jacob Kongsted, Pär Söderhjelm, and Ulf Ryde . Nonpolar Solvation Free Energies of Protein−Ligand Complexes. Journal of Chemical Theory and Computation 2010, 6 (11) , 3558-3568. https://doi.org/10.1021/ct100272s
    42. Wei Jiang and Benoît Roux. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. Journal of Chemical Theory and Computation 2010, 6 (9) , 2559-2565. https://doi.org/10.1021/ct1001768
    43. Emilio Gallicchio, Mauro Lapelosa, and Ronald M. Levy. Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities. Journal of Chemical Theory and Computation 2010, 6 (9) , 2961-2977. https://doi.org/10.1021/ct1002913
    44. Lijun Liu, Walter A. Baase, Miya M. Michael and Brian W. Matthews. Use of Stabilizing Mutations To Engineer a Charged Group within a Ligand-Binding Hydrophobic Cavity in T4 Lysozyme. Biochemistry 2009, 48 (37) , 8842-8851. https://doi.org/10.1021/bi900685j
    45. Matthew Clark, Siavash Meshkat, George T. Talbot, Paolo Carnevali and Jeffrey S. Wiseman. Fragment-Based Computation of Binding Free Energies by Systematic Sampling. Journal of Chemical Information and Modeling 2009, 49 (8) , 1901-1913. https://doi.org/10.1021/ci900132r
    46. Matthew Clark, Sia Meshkat and Jeffrey S. Wiseman. Grand Canonical Free-Energy Calculations of Protein−Ligand Binding. Journal of Chemical Information and Modeling 2009, 49 (4) , 934-943. https://doi.org/10.1021/ci8004397
    47. Daniel A. Kraut, Michael J. Churchill, Phillip E. Dawson and Daniel Herschlag . Evaluating the Potential for Halogen Bonding in the Oxyanion Hole of Ketosteroid Isomerase Using Unnatural Amino Acid Mutagenesis. ACS Chemical Biology 2009, 4 (4) , 269-273. https://doi.org/10.1021/cb900016q
    48. Yuqing Deng and Benoît Roux. Computations of Standard Binding Free Energies with Molecular Dynamics Simulations. The Journal of Physical Chemistry B 2009, 113 (8) , 2234-2246. https://doi.org/10.1021/jp807701h
    49. Seth A. Hayik, Ning Liao and Kenneth M. Merz, Jr. . A Combined QM/MM Poisson−Boltzmann Approach. Journal of Chemical Theory and Computation 2008, 4 (8) , 1200-1207. https://doi.org/10.1021/ct700245a
    50. David L. Mobley,, John D. Chodera, and, Ken A. Dill. Confine-and-Release Method:  Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. Journal of Chemical Theory and Computation 2007, 3 (4) , 1231-1235. https://doi.org/10.1021/ct700032n
    51. Yuqing Deng and, Benoît Roux. Calculation of Standard Binding Free Energies:  Aromatic Molecules in the T4 Lysozyme L99A Mutant. Journal of Chemical Theory and Computation 2006, 2 (5) , 1255-1273. https://doi.org/10.1021/ct060037v
    52. Jens Carlsson and, Johan Åqvist. Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding. The Journal of Physical Chemistry B 2005, 109 (13) , 6448-6456. https://doi.org/10.1021/jp046022f
    53. Andrew Morton, Walter A. Baase, and Brian W. Matthews. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 1995, 34 (27) , 8564-8575. https://doi.org/10.1021/bi00027a006
    54. Miroslav Suruzhon, Khaled Abdel-Maksoud, Michael S. Bodnarchuk, Antonella Ciancetta, Ian D. Wall, Jonathan W. Essex. Enhancing torsional sampling using fully adaptive simulated tempering. The Journal of Chemical Physics 2024, 160 (15) https://doi.org/10.1063/5.0190659
    55. Haohao Fu, Haochuan Chen, Marharyta Blazhynska, Emma Goulard Coderc de Lacam, Florence Szczepaniak, Anna Pavlova, Xueguang Shao, James C. Gumbart, François Dehez, Benoît Roux, Wensheng Cai, Christophe Chipot. Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations. Nature Protocols 2022, 17 (4) , 1114-1141. https://doi.org/10.1038/s41596-021-00676-1
    56. Deeksha Thakur, Shashi Bhushan Pandit. Unusual commonality in active site structural features of substrate promiscuous and specialist enzymes. Journal of Structural Biology 2022, 214 (1) , 107835. https://doi.org/10.1016/j.jsb.2022.107835
    57. Zhaoxi Sun, Payam Kalhor, Yang Xu, Jian Liu. Extensive numerical tests of leapfrog integrator in middle thermostat scheme in molecular simulations. Chinese Journal of Chemical Physics 2021, 34 (6) , 932-948. https://doi.org/10.1063/1674-0068/cjcp2111242
    58. Anna S. Kamenik, Isha Singh, Parnian Lak, Trent E. Balius, Klaus R. Liedl, Brian K. Shoichet. Energy penalties enhance flexible receptor docking in a model cavity. Proceedings of the National Academy of Sciences 2021, 118 (36) https://doi.org/10.1073/pnas.2106195118
    59. Shanshan Y. C. Bradford, Léa El Khoury, Yunhui Ge, Meghan Osato, David L. Mobley, Marcus Fischer. Temperature artifacts in protein structures bias ligand-binding predictions. Chemical Science 2021, 12 (34) , 11275-11293. https://doi.org/10.1039/D1SC02751D
    60. Paulo C. T. Souza, Sebastian Thallmair, Paolo Conflitti, Carlos Ramírez-Palacios, Riccardo Alessandri, Stefano Raniolo, Vittorio Limongelli, Siewert J. Marrink. Protein–ligand binding with the coarse-grained Martini model. Nature Communications 2020, 11 (1) https://doi.org/10.1038/s41467-020-17437-5
    61. Daniel J. Cole, Israel Cabeza de Vaca, William L. Jorgensen. Computation of protein–ligand binding free energies using quantum mechanical bespoke force fields. MedChemComm 2019, 10 (7) , 1116-1120. https://doi.org/10.1039/C9MD00017H
    62. Dheeraj Dube, Navjeet Ahalawat, Himanshu Khandelia, Jagannath Mondal, Surajit Sengupta, . On identifying collective displacements in apo-proteins that reveal eventual binding pathways. PLOS Computational Biology 2019, 15 (1) , e1006665. https://doi.org/10.1371/journal.pcbi.1006665
    63. Victoria A. Feher, Jamie M. Schiffer, Daniel J. Mermelstein, Nathan Mih, Levi C.T. Pierce, J. Andrew McCammon, Rommie E. Amaro. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophysical Journal 2019, 116 (2) , 205-214. https://doi.org/10.1016/j.bpj.2018.09.035
    64. Trung Hai Nguyen, Huan‐Xiang Zhou, David D. L. Minh. Using the fast fourier transform in binding free energy calculations. Journal of Computational Chemistry 2018, 39 (11) , 621-636. https://doi.org/10.1002/jcc.25139
    65. Ariane Nunes-Alves, Daniel M. Zuckerman, Guilherme Menegon Arantes. Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways. Biophysical Journal 2018, 114 (5) , 1058-1066. https://doi.org/10.1016/j.bpj.2018.01.014
    66. Ryo Kitahara, Shun Sakuraba, Tomoshi Kameda, Sanshiro Okuda, Mengjun Xue, Frans A.A. Mulder. Nuclear magnetic resonance‐based determination of dioxygen binding sites in protein cavities. Protein Science 2018, 27 (3) , 769-779. https://doi.org/10.1002/pro.3371
    67. David L. Mobley, Michael K. Gilson. Predicting Binding Free Energies: Frontiers and Benchmarks. Annual Review of Biophysics 2017, 46 (1) , 531-558. https://doi.org/10.1146/annurev-biophys-070816-033654
    68. Takahiro Kawamura, Takuro Wakamoto, Soichiro Kitazawa, Shun Sakuraba, Tomoshi Kameda, Ryo Kitahara. Analysis of O 2 -binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A. Biophysical Journal 2017, 112 (9) , 1820-1828. https://doi.org/10.1016/j.bpj.2017.03.029
    69. Yinglong Miao, J. Andrew McCammon. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications. 2017, 231-278. https://doi.org/10.1016/bs.arcc.2017.06.005
    70. Daniel J. Cole, Matej Janecek, Jamie E. Stokes, Maxim Rossmann, John C. Faver, Grahame J. McKenzie, Ashok R. Venkitaraman, Marko Hyvönen, David R. Spring, David J. Huggins, William L. Jorgensen. Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase–TPX2 protein–protein interaction. Chemical Communications 2017, 53 (67) , 9372-9375. https://doi.org/10.1039/C7CC05379G
    71. Zhao X. Sun, Xiao H. Wang, John Z. H. Zhang. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation. Physical Chemistry Chemical Physics 2017, 19 (23) , 15005-15020. https://doi.org/10.1039/C7CP01561E
    72. Jahan B. Ghasemi, Azizeh Abdolmaleki, Fereshteh Shiri. Molecular Docking Challenges and Limitations. 2017, 770-794. https://doi.org/10.4018/978-1-5225-1762-7.ch030
    73. Jamie M. Schiffer, Victoria A. Feher, Robert D. Malmstrom, Roxana Sida, Rommie E. Amaro. Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. Biophysical Journal 2016, 111 (8) , 1631-1640. https://doi.org/10.1016/j.bpj.2016.08.041
    74. Ryo Kitahara, Yuichi Yoshimura, Mengjun Xue, Tomoshi Kameda, Frans A. A. Mulder. Detecting O2 binding sites in protein cavities. Scientific Reports 2016, 6 (1) https://doi.org/10.1038/srep20534
    75. Jahan B. Ghasemi, Azizeh Abdolmaleki, Fereshteh Shiri. Molecular Docking Challenges and Limitations. 2016, 56-80. https://doi.org/10.4018/978-1-5225-0362-0.ch003
    76. William J. Allen, Trent E. Balius, Sudipto Mukherjee, Scott R. Brozell, Demetri T. Moustakas, P. Therese Lang, David A. Case, Irwin D. Kuntz, Robert C. Rizzo. DOCK 6: Impact of new features and current docking performance. Journal of Computational Chemistry 2015, 36 (15) , 1132-1156. https://doi.org/10.1002/jcc.23905
    77. Michael T. Lerch, Carlos J. López, Zhongyu Yang, Margaux J. Kreitman, Joseph Horwitz, Wayne L. Hubbell. Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure. Proceedings of the National Academy of Sciences 2015, 112 (19) https://doi.org/10.1073/pnas.1506505112
    78. Matthew Merski, Marcus Fischer, Trent E. Balius, Oliv Eidam, Brian K. Shoichet. Homologous ligands accommodated by discrete conformations of a buried cavity. Proceedings of the National Academy of Sciences 2015, 112 (16) , 5039-5044. https://doi.org/10.1073/pnas.1500806112
    79. Akihiro Maeno, Daniel Sindhikara, Fumio Hirata, Renee Otten, Frederick W. Dahlquist, Shigeyuki Yokoyama, Kazuyuki Akasaka, Frans A.A. Mulder, Ryo Kitahara. Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme. Biophysical Journal 2015, 108 (1) , 133-145. https://doi.org/10.1016/j.bpj.2014.11.012
    80. Stephen J. Fox, Jacek Dziedzic, Thomas Fox, Christofer S. Tautermann, Chris‐Kriton Skylaris. Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site. Proteins: Structure, Function, and Bioinformatics 2014, 82 (12) , 3335-3346. https://doi.org/10.1002/prot.24686
    81. Chayan Acharya, Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan. PeptiSite: A structural database of peptide binding sites in 4D. Biochemical and Biophysical Research Communications 2014, 445 (4) , 717-723. https://doi.org/10.1016/j.bbrc.2013.12.132
    82. Sarah Barelier, Sarah E. Boyce, Inbar Fish, Marcus Fischer, David B. Goodin, Brian K. Shoichet, . Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities. PLoS ONE 2013, 8 (7) , e69153. https://doi.org/10.1371/journal.pone.0069153
    83. Dilraj Lama, Vivek Modi, Ramasubbu Sankararamakrishnan, . Behavior of Solvent-Exposed Hydrophobic Groove in the Anti-Apoptotic Bcl-XL Protein: Clues for Its Ability to Bind Diverse BH3 Ligands from MD Simulations. PLoS ONE 2013, 8 (2) , e54397. https://doi.org/10.1371/journal.pone.0054397
    84. David L. Mobley, Pavel V. Klimovich. Perspective: Alchemical free energy calculations for drug discovery. The Journal of Chemical Physics 2012, 137 (23) https://doi.org/10.1063/1.4769292
    85. Liam M. Longo, Michael Blaber. Protein design at the interface of the pre-biotic and biotic worlds. Archives of Biochemistry and Biophysics 2012, 526 (1) , 16-21. https://doi.org/10.1016/j.abb.2012.06.009
    86. Lingle Wang, B. J. Berne, Richard A. Friesner. On achieving high accuracy and reliability in the calculation of relative protein–ligand binding affinities. Proceedings of the National Academy of Sciences 2012, 109 (6) , 1937-1942. https://doi.org/10.1073/pnas.1114017109
    87. Jeff Wereszczynski, J. Andrew McCammon. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Quarterly Reviews of Biophysics 2012, 45 (1) , 1-25. https://doi.org/10.1017/S0033583511000096
    88. T. Christensen, W. Hassouneh, D.J. Callahan, A. Chilkoti. 3.11 Protein Switches. 2012, 238-266. https://doi.org/10.1016/B978-0-12-374920-8.00316-7
    89. Anthony E. Klon, Zenon Konteatis, Siavash N. Meshkat, Jinming Zou, Charles H. Reynolds. Fragment and protein simulation methods in fragment based drug design. Drug Development Research 2011, 72 (2) , 130-137. https://doi.org/10.1002/ddr.20409
    90. Samuel Genheden, Ulf Ryde. A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. Journal of Computational Chemistry 2011, 32 (2) , 187-195. https://doi.org/10.1002/jcc.21546
    91. L. Y. Chen. Exploring the free-energy landscapes of biological systems with steered molecular dynamics. Physical Chemistry Chemical Physics 2011, 13 (13) , 6176. https://doi.org/10.1039/c0cp02799e
    92. Michael R. Shirts, David L. Mobley, Scott P. Brown. Free-energy calculations in structure-based drug design. 2010, 61-86. https://doi.org/10.1017/CBO9780511730412.007
    93. Nidhi Singh, Arieh Warshel. A comprehensive examination of the contributions to the binding entropy of protein–ligand complexes. Proteins: Structure, Function, and Bioinformatics 2010, 78 (7) , 1724-1735. https://doi.org/10.1002/prot.22689
    94. Walter A. Baase, Lijun Liu, Dale E. Tronrud, Brian W. Matthews. Lessons from the lysozyme of phage T4. Protein Science 2010, 19 (4) , 631-641. https://doi.org/10.1002/pro.344
    95. Sarah E. Boyce, David L. Mobley, Gabriel J. Rocklin, Alan P. Graves, Ken A. Dill, Brian K. Shoichet. Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site. Journal of Molecular Biology 2009, 394 (4) , 747-763. https://doi.org/10.1016/j.jmb.2009.09.049
    96. Lijun Liu, Adam J. V. Marwitz, Brian W. Matthews, Shih‐Yuan Liu. Boron Mimetics: 1,2‐Dihydro‐1,2‐azaborines Bind inside a Nonpolar Cavity of T4 Lysozyme. Angewandte Chemie International Edition 2009, 48 (37) , 6817-6819. https://doi.org/10.1002/anie.200903390
    97. Lijun Liu, Adam J. V. Marwitz, Brian W. Matthews, Shih‐Yuan Liu. Boron Mimetics: 1,2‐Dihydro‐1,2‐azaborines Bind inside a Nonpolar Cavity of T4 Lysozyme. Angewandte Chemie 2009, 121 (37) , 6949-6951. https://doi.org/10.1002/ange.200903390
    98. David L. Mobley, Ken A. Dill. Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”. Structure 2009, 17 (4) , 489-498. https://doi.org/10.1016/j.str.2009.02.010
    99. Lijun Liu, Walter A. Baase, Brian W. Matthews. Halogenated Benzenes Bound within a Non-polar Cavity in T4 Lysozyme Provide Examples of I⋯S and I⋯Se Halogen-bonding. Journal of Molecular Biology 2009, 385 (2) , 595-605. https://doi.org/10.1016/j.jmb.2008.10.086
    100. Tomas Rodinger, P. Lynne Howell, Régis Pomès. Calculation of absolute protein-ligand binding free energy using distributed replica sampling. The Journal of Chemical Physics 2008, 129 (15) https://doi.org/10.1063/1.2989800
    Load all citations

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect