151
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Li Y, Li X, Ma W, Dong Z. Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering. J Chem Theory Comput 2014; 10:3503-3511. [PMID: 25136273 PMCID: PMC4132868 DOI: 10.1021/ct500162b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Indexed: 01/15/2023]
Abstract
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The
epidermal growth factor receptor (EGFR) is aberrantly activated
in various cancer cells and an important target for cancer treatment.
Deep understanding of EGFR conformational changes between the active
and inactive states is of pharmaceutical interest. Here we present
a strategy combining multiply targeted molecular dynamics simulations,
unbiased molecular dynamics simulations, and Bayesian clustering to
investigate transition pathways during the activation/inactivation
process of EGFR kinase domain. Two distinct pathways between the active
and inactive forms are designed, explored, and compared. Based on
Bayesian clustering and rough two-dimensional free energy surfaces,
the energy-favorable pathway is recognized, though DFG-flip happens
in both pathways. In addition, another pathway with different intermediate
states appears in our simulations. Comparison of distinct pathways
also indicates that disruption of the Lys745-Glu762 interaction is
critically important in DFG-flip while movement of the A-loop significantly
facilitates the conformational change. Our simulations yield new insights
into EGFR conformational transitions. Moreover, our results verify
that this approach is valid and efficient in sampling of protein conformational
changes and comparison of distinct pathways.
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Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota , Austin, Minnesota 55912, United States
| | - Xiang Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Zhengzhou University , 450001 Zhengzhou, Henan, China
| | - Weiya Ma
- The Hormel Institute, University of Minnesota , Austin, Minnesota 55912, United States
| | - Zigang Dong
- The Hormel Institute, University of Minnesota , Austin, Minnesota 55912, United States
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152
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Pan AC, Weinreich TM, Shan Y, Scarpazza DP, Shaw DE. Assessing the Accuracy of Two Enhanced Sampling Methods Using EGFR Kinase Transition Pathways: The Influence of Collective Variable Choice. J Chem Theory Comput 2014; 10:2860-5. [PMID: 26586510 DOI: 10.1021/ct500223p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Structurally elucidating transition pathways between protein conformations gives deep mechanistic insight into protein behavior but is typically difficult. Unbiased molecular dynamics (MD) simulations provide one solution, but their computational expense is often prohibitive, motivating the development of enhanced sampling methods that accelerate conformational changes in a given direction, embodied in a collective variable. The accuracy of such methods is unclear for complex protein transitions, because obtaining unbiased MD data for comparison is difficult. Here, we use long-time scale, unbiased MD simulations of epidermal growth factor receptor kinase deactivation as a complex biological test case for two widely used methods-steered molecular dynamics (SMD) and the string method. We found that common collective variable choices, based on the root-mean-square deviation (RMSD) of the entire protein, prevented the methods from producing accurate paths, even in SMD simulations on the time scale of the unbiased transition. Using collective variables based on the RMSD of the region of the protein known to be important for the conformational change, however, enabled both methods to provide a more accurate description of the pathway in a fraction of the simulation time required to observe the unbiased transition.
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Affiliation(s)
- Albert C Pan
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - Yibing Shan
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York 10032, United States
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153
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Jiménez-Osés G, Osuna S, Gao X, Sawaya MR, Gilson L, Collier SJ, Huisman GW, Yeates TO, Tang Y, Houk KN. The role of distant mutations and allosteric regulation on LovD active site dynamics. Nat Chem Biol 2014; 10:431-6. [PMID: 24727900 PMCID: PMC4028369 DOI: 10.1038/nchembio.1503] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/13/2014] [Indexed: 01/04/2023]
Abstract
Natural enzymes have evolved to perform their cellular functions under complex selective pressures, which often require their catalytic activities to be regulated by other proteins. We contrasted a natural enzyme, LovD, which acts on a protein-bound (LovF) acyl substrate, with a laboratory-generated variant that was transformed by directed evolution to accept instead a small free acyl thioester and no longer requires the acyl carrier protein. The resulting 29-mutant variant is 1,000-fold more efficient in the synthesis of the drug simvastatin than the wild-type LovD. This is to our knowledge the first nonpatent report of the enzyme currently used for the manufacture of simvastatin as well as the intermediate evolved variants. Crystal structures and microsecond-scale molecular dynamics simulations revealed the mechanism by which the laboratory-generated mutations free LovD from dependence on protein-protein interactions. Mutations markedly altered conformational dynamics of the catalytic residues, obviating the need for allosteric modulation by the acyl carrier LovF.
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Affiliation(s)
- Gonzalo Jiménez-Osés
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569
| | - Sílvia Osuna
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095
| | - Michael R. Sawaya
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - Lynne Gilson
- Codexis, Inc., 200 Penobscot Drive, Redwood City, California 94063
| | | | - Gjalt W. Huisman
- Codexis, Inc., 200 Penobscot Drive, Redwood City, California 94063
| | - Todd O. Yeates
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569
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154
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D'Abramo M, Besker N, Chillemi G, Grottesi A. Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges. Front Genet 2014; 5:128. [PMID: 24860596 PMCID: PMC4026744 DOI: 10.3389/fgene.2014.00128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 04/22/2014] [Indexed: 12/26/2022] Open
Abstract
Protein kinases work because their flexibility allows to continuously switch from inactive to active form. Despite the large number of structures experimentally determined in such states, the mechanism of their conformational transitions as well as the transition pathways are not easily to capture. In this regard, computational methods can help to shed light on such an issue. However, due to the intrinsic sampling limitations, much efforts have been done to model in a realistic way the conformational changes occurring in protein kinases. In this review we will address the principal biological achievements and structural aspects in studying kinases conformational transitions and will focus on the main challenges related to computational approaches such as molecular modeling and MD simulations.
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Affiliation(s)
- Marco D'Abramo
- CINECA Rome, Italy ; Dipartimento di Chimica, Sapienza University of Rome Rome, Italy
| | - Neva Besker
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata," Rome, Italy
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155
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Whitford PC, Sanbonmatsu KY. Simulating movement of tRNA through the ribosome during hybrid-state formation. J Chem Phys 2014; 139:121919. [PMID: 24089731 DOI: 10.1063/1.4817212] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Biomolecular simulations provide a means for exploring the relationship between flexibility, energetics, structure, and function. With the availability of atomic models from X-ray crystallography and cryoelectron microscopy (cryo-EM), and rapid increases in computing capacity, it is now possible to apply molecular dynamics (MD) simulations to large biomolecular machines, and systematically partition the factors that contribute to function. A large biomolecular complex for which atomic models are available is the ribosome. In the cell, the ribosome reads messenger RNA (mRNA) in order to synthesize proteins. During this essential process, the ribosome undergoes a wide range of conformational rearrangements. One of the most poorly understood transitions is translocation: the process by which transfer RNA (tRNA) molecules move between binding sites inside of the ribosome. The first step of translocation is the adoption of a "hybrid" configuration by the tRNAs, which is accompanied by large-scale rotations in the ribosomal subunits. To illuminate the relationship between these rearrangements, we apply MD simulations using a multi-basin structure-based (SMOG) model, together with targeted molecular dynamics protocols. From 120 simulated transitions, we demonstrate the viability of a particular route during P/E hybrid-state formation, where there is asynchronous movement along rotation and tRNA coordinates. These simulations not only suggest an ordering of events, but they highlight atomic interactions that may influence the kinetics of hybrid-state formation. From these simulations, we also identify steric features (H74 and surrounding residues) encountered during the hybrid transition, and observe that flexibility of the single-stranded 3'-CCA tail is essential for it to reach the endpoint. Together, these simulations provide a set of structural and energetic signatures that suggest strategies for modulating the physical-chemical properties of protein synthesis by the ribosome.
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Affiliation(s)
- Paul C Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
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156
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Vashisth H, Skiniotis G, Brooks CL. Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chem Rev 2014; 114:3353-65. [PMID: 24446720 PMCID: PMC3983124 DOI: 10.1021/cr4005988] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Harish Vashisth
- Department
of Chemical Engineering, University of New
Hampshire, Durham, New Hampshire 03824, United States
| | - Georgios Skiniotis
- Life Sciences Institute, Department
of Biological Chemistry, and
Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles Lee Brooks
- Life Sciences Institute, Department
of Biological Chemistry, and
Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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157
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Fang J, Nevin P, Kairys V, Venclovas Č, Engen JR, Beuning PJ. Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics. Structure 2014; 22:572-581. [PMID: 24613485 DOI: 10.1016/j.str.2014.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/23/2014] [Accepted: 02/01/2014] [Indexed: 02/06/2023]
Abstract
The relationship between protein sequence, structure, and dynamics has been elusive. Here, we report a comprehensive analysis using an in-solution experimental approach to study how the conservation of tertiary structure correlates with protein dynamics. Hydrogen exchange measurements of eight processivity clamp proteins from different species revealed that, despite highly similar three-dimensional structures, clamp proteins display a wide range of dynamic behavior. Differences were apparent both for structurally similar domains within proteins and for corresponding domains of different proteins. Several of the clamps contained regions that underwent local unfolding with different half-lives. We also observed a conserved pattern of alternating dynamics of the α helices lining the inner pore of the clamps as well as a correlation between dynamics and the number of salt bridges in these α helices. Our observations reveal that tertiary structure and dynamics are not directly correlated and that primary structure plays an important role in dynamics.
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Affiliation(s)
- Jing Fang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Philip Nevin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Visvaldas Kairys
- Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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158
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Sours KM, Xiao Y, Ahn NG. Extracellular-regulated kinase 2 is activated by the enhancement of hinge flexibility. J Mol Biol 2014; 426:1925-35. [PMID: 24534729 DOI: 10.1016/j.jmb.2014.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 11/17/2022]
Abstract
Protein motions underlie conformational and entropic contributions to enzyme catalysis; however, relatively little is known about the ways in which this occurs. Studies of the mitogen-activated protein kinase ERK2 (extracellular-regulated protein kinase 2) by hydrogen-exchange mass spectrometry suggest that activation enhances backbone flexibility at the linker between N- and C-terminal domains while altering nucleotide binding mode. Here, we address the hypothesis that enhanced backbone flexibility within the hinge region facilitates kinase activation. We show that hinge mutations enhancing flexibility promote changes in the nucleotide binding mode consistent with domain movement, without requiring phosphorylation. They also lead to the activation of monophosphorylated ERK2, a form that is normally inactive. The hinge mutations bypass the need for pTyr but not pThr, suggesting that Tyr phosphorylation controls hinge motions. In agreement, monophosphorylation of pTyr enhances both hinge flexibility and nucleotide binding mode, measured by hydrogen-exchange mass spectrometry. Our findings demonstrate that regulated protein motions underlie kinase activation. Our working model is that constraints to domain movement in ERK2 are overcome by phosphorylation at pTyr, which increases hinge dynamics to promote the active conformation of the catalytic site.
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Affiliation(s)
- Kevin M Sours
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Yao Xiao
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Natalie G Ahn
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA.
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159
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Abstract
Protein motions control enzyme catalysis through mechanisms that are incompletely understood. Here NMR (13)C relaxation dispersion experiments were used to monitor changes in side-chain motions that occur in response to activation by phosphorylation of the MAP kinase ERK2. NMR data for the methyl side chains on Ile, Leu, and Val residues showed changes in conformational exchange dynamics in the microsecond-to-millisecond time regime between the different activity states of ERK2. In inactive, unphosphorylated ERK2, localized conformational exchange was observed among methyl side chains, with little evidence for coupling between residues. Upon dual phosphorylation by MAP kinase kinase 1, the dynamics of assigned methyls in ERK2 were altered throughout the conserved kinase core, including many residues in the catalytic pocket. The majority of residues in active ERK2 fit to a single conformational exchange process, with kex ≈ 300 s(-1) (kAB ≈ 240 s(-1)/kBA ≈ 60 s(-1)) and pA/pB ≈ 20%/80%, suggesting global domain motions involving interconversion between two states. A mutant of ERK2, engineered to enhance conformational mobility at the hinge region linking the N- and C-terminal domains, also induced two-state conformational exchange throughout the kinase core, with exchange properties of kex ≈ 500 s(-1) (kAB ≈ 15 s(-1)/kBA ≈ 485 s(-1)) and pA/pB ≈ 97%/3%. Thus, phosphorylation and activation of ERK2 lead to a dramatic shift in conformational exchange dynamics, likely through release of constraints at the hinge.
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160
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Abstract
In recent years, HDX-MS (hydrogen–deuterium exchange coupled to MS) on biomolecules has evolved from a niche technique to a powerful method in the investigation of protein dynamics. Protein kinases, in particular, represent an area of active study using this technique owing to their well-characterized protein structures and their relevance to diseases such as cancer, immune disorders and neurodegenerative defects. In the present review, we describe how HDX-MS has revealed important dynamic properties of protein kinases and provided insight into the mechanisms of drug binding.
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161
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Buch I, Ferruz N, De Fabritiis G. Computational modeling of an epidermal growth factor receptor single-mutation resistance to cetuximab in colorectal cancer treatment. J Chem Inf Model 2013; 53:3123-6. [PMID: 24219403 DOI: 10.1021/ci400456m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Extracellular S468R mutation of the epidermal growth factor receptor (EGFR) was recently identified as the cause of resistance to cetuximab, a widely used drug in colorectal cancer treatment. Here, we have determined the binding free energies of cetuximab's Fab V(H)-V(L) domains and endogenous EGF ligand to wild type and S468R EGFR by high-throughput molecular dynamics. This work provides a possible mechanism of resistance in terms of increased competition, an hypothesis that can be further validated experimentally.
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Affiliation(s)
- Ignasi Buch
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra , Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
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162
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Jhoti H, Rees S, Solari R. High-throughput screening and structure-based approaches to hit discovery: is there a clear winner? Expert Opin Drug Discov 2013; 8:1449-53. [DOI: 10.1517/17460441.2013.857654] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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163
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Activating Janus kinase pseudokinase domain mutations in myeloproliferative and other blood cancers. Biochem Soc Trans 2013; 41:1048-54. [DOI: 10.1042/bst20130084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The discovery of the highly prevalent activating JAK (Janus kinase) 2 V617F mutation in myeloproliferative neoplasms, and of other pseudokinase domain-activating mutations in JAK2, JAK1 and JAK3 in blood cancers, prompted great interest in understanding how pseudokinase domains regulate kinase domains in JAKs. Recent functional and mutagenesis studies identified residues required for the V617F mutation to induce activation. Several X-ray crystal structures of either kinase or pseudokinase domains including the V617F mutant of JAK2 pseudokinase domains are now available, and a picture has emerged whereby the V617F mutation induces a defined conformational change around helix C of JH (JAK homology) 2. Effects of mutations on JAK2 can be extrapolated to JAK1 and TYK2 (tyrosine kinase 2), whereas JAK3 appears to be different. More structural information of the full-length JAK coupled to cytokine receptors might be required in order to define the structural basis of JH1 activation by JH2 mutants and eventually obtain mutant-specific inhibitors.
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164
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Zhu S, Travis SM, Elcock AH. Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study. J Chem Theory Comput 2013; 9:3151-3164. [PMID: 23914145 PMCID: PMC3731164 DOI: 10.1021/ct400104x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A major current challenge for drug design efforts focused on protein kinases is the development of drug resistance caused by spontaneous mutations in the kinase catalytic domain. The ubiquity of this problem means that it would be advantageous to develop fast, effective computational methods that could be used to determine the effects of potential resistance-causing mutations before they arise in a clinical setting. With this long-term goal in mind, we have conducted a combined experimental and computational study of the thermodynamic effects of active-site mutations on a well-characterized and high-affinity interaction between a protein kinase and a small-molecule inhibitor. Specifically, we developed a fluorescence-based assay to measure the binding free energy of the small-molecule inhibitor, SB203580, to the p38α MAP kinase and used it measure the inhibitor's affinity for five different kinase mutants involving two residues (Val38 and Ala51) that contact the inhibitor in the crystal structure of the inhibitor-kinase complex. We then conducted long, explicit-solvent thermodynamic integration (TI) simulations in an attempt to reproduce the experimental relative binding affinities of the inhibitor for the five mutants; in total, a combined simulation time of 18.5 μs was obtained. Two widely used force fields - OPLS-AA/L and Amber ff99SB-ILDN - were tested in the TI simulations. Both force fields produced excellent agreement with experiment for three of the five mutants; simulations performed with the OPLS-AA/L force field, however, produced qualitatively incorrect results for the constructs that contained an A51V mutation. Interestingly, the discrepancies with the OPLS-AA/L force field could be rectified by the imposition of position restraints on the atoms of the protein backbone and the inhibitor without destroying the agreement for other mutations; the ability to reproduce experiment depended, however, upon the strength of the restraints' force constant. Imposition of position restraints in corresponding simulations that used the Amber ff99SB-ILDN force field had little effect on their ability to match experiment. Overall, the study shows that both force fields can work well for predicting the effects of active-site mutations on small molecule binding affinities and demonstrates how a direct combination of experiment and computation can be a powerful strategy for developing an understanding of protein-inhibitor interactions.
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Affiliation(s)
- Shun Zhu
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
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165
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Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase. Proc Natl Acad Sci U S A 2013; 110:10616-21. [PMID: 23754386 DOI: 10.1073/pnas.1221953110] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Activating mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase are frequently found in many cancers. It has been suggested that changes in the equilibrium between its active and inactive conformations are linked to its oncogenic potential. Here, we quantify the effects of some of the most common single (L858R and T790M) and double (T790M-L858R) oncogenic mutations on the conformational free-energy landscape of the EGFR kinase domain by using massive molecular dynamics simulations together with parallel tempering, metadynamics, and one of the best force-fields available. Whereas the wild-type EGFR catalytic domain monomer is mostly found in an inactive conformation, our results show a clear shift toward the active conformation for all of the mutants. The L858R mutation stabilizes the active conformation at the expense of the inactive conformation and rigidifies the αC-helix. The T790M gatekeeper mutant favors activation by stabilizing a hydrophobic cluster. Finally, T790M with L858R shows a significant positive epistasis effect. This combination not only stabilizes the active conformation, but in nontrivial ways changes the free-energy landscape lowering the transition barriers.
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166
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