1
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Kneller DW, Gerlits O, Daemen LL, Pavlova A, Gumbart JC, Cheng Y, Kovalevsky A. Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor. Phys Chem Chem Phys 2022; 24:3586-3597. [PMID: 35089990 PMCID: PMC8940534 DOI: 10.1039/d1cp05487b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ∼5-50 cm-1. This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effects of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal mol-1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, U.S.A
| | - Luke L. Daemen
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Yongqiang Cheng
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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2
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Dandekar BR, Ahalawat N, Mondal J. Reconciling conformational heterogeneity and substrate recognition in cytochrome P450. Biophys J 2021; 120:1732-1745. [PMID: 33675756 PMCID: PMC8204291 DOI: 10.1016/j.bpj.2021.02.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450, the ubiquitous metalloenzyme involved in detoxification of foreign components, has remained one of the most popular systems for substrate-recognition process. However, despite being known for its high substrate specificity, the mechanistic basis of substrate-binding by archetypal system cytochrome P450cam has remained at odds with the contrasting reports of multiple diverse crystallographic structures of its substrate-free form. Here, we address this issue by elucidating the probability of mutual dynamical transition to the other crystallographic pose of cytochrome P450cam and vice versa via unbiased all-atom computer simulation. A robust Markov state model, constructed using adaptively sampled 84-μs-long molecular dynamics simulation trajectories, maps the broad and heterogenous P450cam conformational landscape into five key substates. In particular, the Markov state model identifies an intermediate-assisted dynamic equilibrium between a pair of conformations of P450cam, in which the substrate-recognition sites remain "closed" and "open," respectively. However, the estimate of a significantly higher stationary population of closed conformation, coupled with faster rate of open → closed transition than its reverse process, dictates that the net conformational equilibrium would be swayed in favor of "closed" conformation. Together, the investigation quantitatively infers that although a potential substrate of cytochrome P450cam would, in principle, explore a diverse array of conformations of substrate-free protein, it would mostly encounter a "closed" or solvent-occluded conformation and hence would follow an induced-fit-based recognition process. Overall, the work reconciles multiple precedent crystallographic, spectroscopic investigations and establishes how a statistical elucidation of conformational heterogeneity in protein would provide crucial insights in the mechanism of potential substrate-recognition process.
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Affiliation(s)
- Bhupendra R Dandekar
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, India
| | - Navjeet Ahalawat
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, India.
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3
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Ramos S, Mammoser CC, Thibodeau KE, Thielges MC. Dynamics underlying hydroxylation selectivity of cytochrome P450cam. Biophys J 2021; 120:912-923. [PMID: 33545101 PMCID: PMC8008267 DOI: 10.1016/j.bpj.2021.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 10/22/2022] Open
Abstract
Structural heterogeneity and the dynamics of the complexes of enzymes with substrates can determine the selectivity of catalysis; however, fully characterizing how remains challenging as heterogeneity and dynamics can vary at the spatial level of an amino acid residue and involve rapid timescales. We demonstrate the nascent approach of site-specific two-dimensional infrared (IR) spectroscopy to investigate the archetypical cytochrome P450, P450cam, to better delineate the mechanism of the lower regioselectivity of hydroxylation of the substrate norcamphor in comparison to the native substrate camphor. Specific locations are targeted throughout the enzyme by selectively introducing cyano groups that have frequencies in a spectrally isolated region of the protein IR spectrum as local vibrational probes. Linear and two-dimensional IR spectroscopy were applied to measure the heterogeneity and dynamics at each probe and investigate how they differentiate camphor and norcamphor recognition. The IR data indicate that the norcamphor complex does not fully induce a large-scale conformational change to a closed state of the enzyme adopted in the camphor complex. Additionally, a probe directed at the bound substrate experiences rapidly interconverting states in the norcamphor complex that explain the hydroxylation product distribution. Altogether, the study reveals large- and small-scale structural heterogeneity and dynamics that could contribute to selectivity of a cytochrome P450 and illustrates the approach of site-selective IR spectroscopy to elucidate protein dynamics.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, Indiana
| | | | | | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana.
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4
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Dajnowicz S, Cheng Y, Daemen LL, Weiss KL, Gerlits O, Mueser TC, Kovalevsky A. Substrate Binding Stiffens Aspartate Aminotransferase by Altering the Enzyme Picosecond Vibrational Dynamics. ACS OMEGA 2020; 5:18787-18797. [PMID: 32775880 PMCID: PMC7408236 DOI: 10.1021/acsomega.0c01900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Protein dynamics on various time scales from femtoseconds to milliseconds impacts biological function by driving proteins to conformations conducive to ligand binding and creating functional states in enzyme catalysis. Neutron vibrational spectroscopy carried out by measuring inelastic neutron scattering from protein molecules in combination with molecular simulations has the unique ability of detecting and visualizing changes in the picosecond protein vibrational dynamics due to ligand binding. Here we present neutron vibrational spectra of a homodimeric pyridoxal 5'-phosphate-dependent enzyme, aspartate aminotransferase, obtained from the open internal aldimine and closed external aldimine conformational states. We observe that in the external aldimine state the protein structure stiffens relative to the internal aldimine state, indicating rigidified vibrational dynamics on the picosecond time scale in the low-frequency regime of 5-50 cm-1. Our molecular dynamics simulations indicate substantial changes in the picosecond dynamics of the enzyme secondary structure elements upon substrate binding, with the largest contributions from just two helices and the β-sheet.
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Affiliation(s)
- Steven Dajnowicz
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
- Department
of Chemistry and Biochemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Yongqiang Cheng
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Luke L. Daemen
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Kevin L. Weiss
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Oksana Gerlits
- Department
of Natural Sciences, Tennessee Wesleyan
University, Athens, Tennessee 37303, United States
| | - Timothy C. Mueser
- Department
of Chemistry and Biochemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Andrey Kovalevsky
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
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5
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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6
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Entropic contribution to enhanced thermal stability in the thermostable P450 CYP119. Proc Natl Acad Sci U S A 2018; 115:E10049-E10058. [PMID: 30297413 PMCID: PMC6205451 DOI: 10.1073/pnas.1807473115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enhanced thermostability of thermophilic proteins with respect to their mesophilic counterparts is often attributed to the enthalpy effect, arising from strong interactions between protein residues. Intuitively, these strong interresidue interactions will rigidify the biomolecules. However, the present work utilizing neutron scattering and solution NMR spectroscopy measurements demonstrates a contrary example that the thermophilic cytochrome P450, CYP119, is much more flexible than its mesophilic counterpart, CYP101A1, something which is not apparent just from structural comparison of the two proteins. A mechanism to explain this apparent contradiction is that higher flexibility in the folded state of CYP119 increases its conformational entropy and thereby reduces the entropy gain during denaturation, which will increase the free energy needed for unfolding and thus stabilize the protein. This scenario is supported by thermodynamic data on the temperature dependence of unfolding free energy, which shows a significant entropic contribution to the thermostability of CYP119 and lends an added dimension to enhanced stability, previously attributed only to presence of aromatic stacking interactions and salt bridge networks. Our experimental data also support the notion that highly thermophilic P450s such as CYP119 may use a mechanism that partitions flexibility differently from mesophilic P450s between ligand binding and thermal stability.
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7
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Abstract
Recent studies demonstrated that Gaussian accelerated molecular dynamics (GaMD) is a robust computational technique, which provides simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. However, the exact acceleration of biomolecular dynamics or speedup of kinetic rates in GaMD simulations and, more broadly, in enhanced sampling methods, remains a challenging task to be determined. Here, the GaMD acceleration is examined using alanine dipeptide in explicit solvent as a biomolecular model system. Relative to long conventional molecular dynamics simulation, GaMD simulations exhibited ∼36-67 times speedup for sampling of the backbone dihedral transitions. The acceleration depended on level of the GaMD boost potential. Furthermore, Kramers' rate theory was applied to estimate GaMD acceleration using simulation-derived diffusion coefficients, curvatures and barriers of free energy profiles. In most cases, the calculations also showed significant speedup of dihedral transitions in GaMD, although the GaMD acceleration factors tended to be underestimated by ∼3-96 fold. Because greater boost potential can be applied in GaMD simulations of systems with increased sizes, which potentially leads to higher acceleration, it is subject to future studies on accelerating the dynamics and recovering kinetic rates of larger biomolecules such as proteins and protein-protein/nucleic acid complexes.
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Affiliation(s)
- Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
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8
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Andersson CD, Martinez N, Zeller D, Allgardsson A, Koza MM, Frick B, Ekström F, Peters J, Linusson A. Influence of Enantiomeric Inhibitors on the Dynamics of Acetylcholinesterase Measured by Elastic Incoherent Neutron Scattering. J Phys Chem B 2018; 122:8516-8525. [DOI: 10.1021/acs.jpcb.8b05485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | - Nicolas Martinez
- Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
- Université Grenoble Alpes, IBS and LiPhy, F-38000 Grenoble, France
| | - Dominik Zeller
- Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
- Université Grenoble Alpes, IBS and LiPhy, F-38000 Grenoble, France
| | - Anders Allgardsson
- CBRN Defence and Security, Swedish Defence Research Agency, SE-90621 Umeå, Sweden
| | | | - Bernhard Frick
- Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
| | - Fredrik Ekström
- CBRN Defence and Security, Swedish Defence Research Agency, SE-90621 Umeå, Sweden
| | - Judith Peters
- Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
- Université Grenoble Alpes, IBS and LiPhy, F-38000 Grenoble, France
| | - Anna Linusson
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
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9
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Abstract
Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed.
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Affiliation(s)
- Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Andersson CD, Martinez N, Zeller D, Rondahl SH, Koza MM, Frick B, Ekström F, Peters J, Linusson A. Changes in dynamics of α-chymotrypsin due to covalent inhibitors investigated by elastic incoherent neutron scattering. Phys Chem Chem Phys 2017; 19:25369-25379. [DOI: 10.1039/c7cp04041e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of chymotrypsin increases when bound to two different covalent inhibitors. These effects were analyzed by univariate and multivariate methods.
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Affiliation(s)
| | - N. Martinez
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - D. Zeller
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - S. H. Rondahl
- CBRN Defence and Security
- Swedish Defence Research Agency
- SE-90621 Umeå
- Sweden
| | - M. M. Koza
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
| | - B. Frick
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
| | - F. Ekström
- CBRN Defence and Security
- Swedish Defence Research Agency
- SE-90621 Umeå
- Sweden
| | - J. Peters
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - A. Linusson
- Department of Chemistry
- Umeå University
- SE-90187 Umeå
- Sweden
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11
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Hong L, Jain N, Cheng X, Bernal A, Tyagi M, Smith JC. Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. SCIENCE ADVANCES 2016; 2:e1600886. [PMID: 27757419 PMCID: PMC5065251 DOI: 10.1126/sciadv.1600886] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.
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Affiliation(s)
- Liang Hong
- Institute of Natural Sciences and Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Nitin Jain
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaolin Cheng
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Ana Bernal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Jeremy C. Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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12
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Miao Y, McCammon JA. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review. MOLECULAR SIMULATION 2016; 42:1046-1055. [PMID: 27453631 PMCID: PMC4955644 DOI: 10.1080/08927022.2015.1121541] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.
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Affiliation(s)
- Yinglong Miao
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - J. Andrew McCammon
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
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13
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Vural D, Hu X, Lindner B, Jain N, Miao Y, Cheng X, Liu Z, Hong L, Smith JC. Quasielastic neutron scattering in biology: Theory and applications. Biochim Biophys Acta Gen Subj 2016; 1861:3638-3650. [PMID: 27316321 DOI: 10.1016/j.bbagen.2016.06.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 02/03/2023]
Abstract
Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Derya Vural
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaohu Hu
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Benjamin Lindner
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Nitin Jain
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Yinglong Miao
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaolin Cheng
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Zhuo Liu
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Liang Hong
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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14
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Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models. Nat Chem 2016; 8:419-25. [PMID: 27102675 PMCID: PMC4843824 DOI: 10.1038/nchem.2474] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
Abstract
The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding, and even dramatically impact enzyme function. When these flexible regions are structurally unresolvable, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here, we present a collaborative approach consisting of both experiment and computation that led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate.
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15
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Miao Y, Baudry J, Smith JC, McCammon JA. General trends of dihedral conformational transitions in a globular protein. Proteins 2016; 84:501-14. [PMID: 26799251 DOI: 10.1002/prot.24996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/28/2015] [Accepted: 01/08/2016] [Indexed: 11/06/2022]
Abstract
Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.
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Affiliation(s)
- Yinglong Miao
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, 92093.,Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093
| | - Jerome Baudry
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - J Andrew McCammon
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, 92093.,Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, 92093
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16
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Dorner ME, McMunn RD, Bartholow TG, Calhoon BE, Conlon MR, Dulli JM, Fehling SC, Fisher CR, Hodgson SW, Keenan SW, Kruger AN, Mabin JW, Mazula DL, Monte CA, Olthafer A, Sexton AE, Soderholm BR, Strom AM, Hati S. Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis. Protein Sci 2015; 24:1495-507. [PMID: 26130403 DOI: 10.1002/pro.2737] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/18/2015] [Accepted: 06/14/2015] [Indexed: 12/24/2022]
Abstract
Cytochrome P450 enzymes are hemeproteins that catalyze the monooxygenation of a wide-range of structurally diverse substrates of endogenous and exogenous origin. These heme monooxygenases receive electrons from NADH/NADPH via electron transfer proteins. The cytochrome P450 enzymes, which constitute a diverse superfamily of more than 8,700 proteins, share a common tertiary fold but < 25% sequence identity. Based on their electron transfer protein partner, cytochrome P450 proteins are classified into six broad classes. Traditional methods of pro are based on the canonical paradigm that attributes proteins' function to their three-dimensional structure, which is determined by their primary structure that is the amino acid sequence. It is increasingly recognized that protein dynamics play an important role in molecular recognition and catalytic activity. As the mobility of a protein is an intrinsic property that is encrypted in its primary structure, we examined if different classes of cytochrome P450 enzymes display any unique patterns of intrinsic mobility. Normal mode analysis was performed to characterize the intrinsic dynamics of five classes of cytochrome P450 proteins. The present study revealed that cytochrome P450 enzymes share a strong dynamic similarity (root mean squared inner product > 55% and Bhattacharyya coefficient > 80%), despite the low sequence identity (< 25%) and sequence similarity (< 50%) across the cytochrome P450 superfamily. Noticeable differences in Cα atom fluctuations of structural elements responsible for substrate binding were noticed. These differences in residue fluctuations might be crucial for substrate selectivity in these enzymes.
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Affiliation(s)
- Mariah E Dorner
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Ryan D McMunn
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Thomas G Bartholow
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Brecken E Calhoon
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Michelle R Conlon
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Jessica M Dulli
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Samuel C Fehling
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Cody R Fisher
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Shane W Hodgson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Shawn W Keenan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Alyssa N Kruger
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Justin W Mabin
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Daniel L Mazula
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Christopher A Monte
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Augustus Olthafer
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Ashley E Sexton
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Beatrice R Soderholm
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Alexander M Strom
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
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17
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Abstract
The energy landscapes of proteins are highly complex and can be influenced by changes in physical and chemical conditions under which the protein is studied. The redox enzyme cytochrome P450cam undergoes a multistep catalytic cycle wherein two electrons are transferred to the heme group and the enzyme visits several conformational states. Using paramagnetic NMR spectroscopy with a lanthanoid tag, we show that the enzyme bound to its redox partner, putidaredoxin, is in a closed state at ambient temperature in solution. This result contrasts with recent crystal structures of the complex, which suggest that the enzyme opens up when bound to its partner. The closed state supports a model of catalysis in which the substrate is locked in the active site pocket and the enzyme acts as an insulator for the reactive intermediates of the reaction.
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18
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González-Andrade M, Rodríguez-Sotres R, Madariaga-Mazón A, Rivera-Chávez J, Mata R, Sosa-Peinado A, Del Pozo-Yauner L, Arias-Olguín II. Insights into molecular interactions between CaM and its inhibitors from molecular dynamics simulations and experimental data. J Biomol Struct Dyn 2015; 34:78-91. [PMID: 25702612 DOI: 10.1080/07391102.2015.1022225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In order to contribute to the structural basis for rational design of calmodulin (CaM) inhibitors, we analyzed the interaction of CaM with 14 classic antagonists and two compounds that do not affect CaM, using docking and molecular dynamics (MD) simulations, and the data were compared to available experimental data. The Ca(2+)-CaM-Ligands complexes were simulated 20 ns, with CaM starting in the "open" and "closed" conformations. The analysis of the MD simulations provided insight into the conformational changes undergone by CaM during its interaction with these ligands. These simulations were used to predict the binding free energies (ΔG) from contributions ΔH and ΔS, giving useful information about CaM ligand binding thermodynamics. The ΔG predicted for the CaM's inhibitors correlated well with available experimental data as the r(2) obtained was 0.76 and 0.82 for the group of xanthones. Additionally, valuable information is presented here: I) CaM has two preferred ligand binding sites in the open conformation known as site 1 and 4, II) CaM can bind ligands of diverse structural nature, III) the flexibility of CaM is reduced by the union of its ligands, leading to a reduction in the Ca(2+)-CaM entropy, IV) enthalpy dominates the molecular recognition process in the system Ca(2+)-CaM-Ligand, and V) the ligands making more extensive contact with the protein have higher affinity for Ca(2+)-CaM. Despite their limitations, docking and MD simulations in combination with experimental data continue to be excellent tools for research in pharmacology, toward a rational design of new drugs.
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Affiliation(s)
- Martin González-Andrade
- a Facultad de Medicina , Universidad Nacional Autónoma de México (UNAM) , México Distrito Federal , CP 04510 , México.,c Unidad de Vinculación de la Facultad de Medicina , UNAM en el INMEGEN , Secretaría de Salud, México Distrito Federal , CP 14610 , México
| | - Rogelio Rodríguez-Sotres
- b Facultad de Química , Universidad Nacional Autónoma de México (UNAM) , México Distrito Federal , CP 04510 , México
| | - Abraham Madariaga-Mazón
- b Facultad de Química , Universidad Nacional Autónoma de México (UNAM) , México Distrito Federal , CP 04510 , México
| | - José Rivera-Chávez
- b Facultad de Química , Universidad Nacional Autónoma de México (UNAM) , México Distrito Federal , CP 04510 , México
| | - Rachel Mata
- b Facultad de Química , Universidad Nacional Autónoma de México (UNAM) , México Distrito Federal , CP 04510 , México
| | - Alejandro Sosa-Peinado
- a Facultad de Medicina , Universidad Nacional Autónoma de México (UNAM) , México Distrito Federal , CP 04510 , México
| | - Luis Del Pozo-Yauner
- c Unidad de Vinculación de la Facultad de Medicina , UNAM en el INMEGEN , Secretaría de Salud, México Distrito Federal , CP 14610 , México
| | - Imilla I Arias-Olguín
- d Unidad de Biología Molecular y Medicina Genómica del Instituto de Investigaciones Biomédicas de la Universidad Nacional Autónoma de México (UNAM) , México Distrito Federal , CP 04510 , México.,e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , México Distrito Federal , CP 14000 , México
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19
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Yu X, Cojocaru V, Mustafa G, Salo-Ahen OMH, Lepesheva GI, Wade RC. Dynamics of CYP51: implications for function and inhibitor design. J Mol Recognit 2015; 28:59-73. [PMID: 25601796 DOI: 10.1002/jmr.2412] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/14/2014] [Accepted: 07/24/2014] [Indexed: 12/12/2022]
Abstract
Sterol 14α-demethylase (cytochrome P450 family 51 (CYP51)) is an essential enzyme occurring in all biological kingdoms. In eukaryotes, it is located in the membrane of the endoplasmic reticulum. Selective inhibitors of trypanosomal CYP51s that do not affect the human CYP51 have been discovered in vitro and found to cure acute and chronic mouse Chagas disease without severe side effects in vivo. Crystal structures indicate that CYP51 may be more rigid than most CYPs, and it has been proposed that this property may facilitate antiparasitic drug design. Therefore, to investigate the dynamics of trypanosomal CYP51, we built a model of membrane-bound Trypanosoma brucei CYP51 and then performed molecular dynamics simulations of T. brucei CYP51 in membrane-bound and soluble forms. We compared the dynamics of T. brucei CYP51 with those of human CYP51, CYP2C9, and CYP2E1. In the simulations, the CYP51s display low mobility in the buried active site although overall mobility is similar in all the CYPs studied. The simulations suggest that in CYP51, pathway 2f serves as the major ligand access tunnel, and both pathways 2f (leading to membrane) and S (leading to solvent) can serve as ligand egress tunnels. Compared with the other CYPs, the residues at the entrance of the ligand access tunnels in CYP51 have higher mobility that may be necessary to facilitate the passage of its large sterol ligands. The water (W) tunnel is accessible to solvent during most of the simulations of CYP51, but its width is affected by the conformations of the heme's two propionate groups. These differ from those observed in the other CYPs studied because of differences in their hydrogen-bonding network. Our simulations give insights into the dynamics of CYP51 that complement the available experimental data and have implications for drug design against CYP51 enzymes.
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Affiliation(s)
- Xiaofeng Yu
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
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20
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Hong L, Petridis L, Smith JC. Biomolecular Structure and Dynamics with Neutrons: The View from Simulation. Isr J Chem 2014. [DOI: 10.1002/ijch.201300137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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21
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Madrona Y, Hollingsworth SA, Khan B, Poulos TL. P450cin active site water: implications for substrate binding and solvent accessibility. Biochemistry 2013; 52:5039-50. [PMID: 23829586 DOI: 10.1021/bi4006946] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In P450cin, Tyr81, Asp241, Asn242, two water molecules, and the substrate participate in a complex H-bonded network. The role of this H-bonded network in substrate binding and catalysis has been probed by crystallography, spectroscopy, kinetics, isothermal titration calorimetry (ITC), and molecular dynamics. For the Y81F mutant, the substrate binds about 20-fold more weakly and Vmax decreases by about 30% in comparison to WT. The enhanced susceptibility of the heme to H₂O₂-mediated destruction in Y81F suggests that this mutant favors the open, low-spin conformational state. Asn242 H-bonds directly with the substrate, and replacing this residue with Ala results in water taking the place of the missing Asn side chain. This mutant exhibits a 70% decrease in activity. Crystal structures and molecular dynamics simulations of substrate-bound complexes show that the solvent has more ready access to the active site, especially for the N242A mutant. This accounts for about a 64% uncoupling of electron transfer from substrate hydroxylation. These data indicate the importance of the interconnected water network on substrate binding and on the open/closed conformational equilibrium, which are both critically important for maintaining high-coupling efficiency.
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Affiliation(s)
- Yarrow Madrona
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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22
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Miao Y, Hong L, Yi Z, Smith JC. Zaccai neutron resilience and site-specific hydration dynamics in a globular protein. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:72. [PMID: 23852576 DOI: 10.1140/epje/i2013-13072-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 01/18/2013] [Accepted: 02/20/2013] [Indexed: 06/02/2023]
Abstract
A discussion is presented of contributions of the Zaccai group to the understanding of flexibility in biological macromolecules using dynamic neutron scattering. The concept of resilience as introduced by Zaccai is discussed and investigated using molecular dynamics simulation on camphor-bound cytochrome P450. The resilience of hydrophilic residues is found to be more strongly affected by hydration than that of hydrophobic counterparts. The hydration-induced softening of protein propagates from the surface into the dry core. Moreover, buried hydrophilic residues behave more like those exposed on the protein surface, and are different from their hydrophobic counterparts.
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Affiliation(s)
- Yinglong Miao
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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23
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Miao Y, Yi Z, Glass DC, Hong L, Tyagi M, Baudry J, Jain N, Smith JC. Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein. J Am Chem Soc 2012; 134:19576-9. [DOI: 10.1021/ja3097898] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yinglong Miao
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Zheng Yi
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dennis C. Glass
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Graduate School of Genome Science
and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Liang Hong
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899, United States
- Department of Materials Science, University of Maryland, College Park, Maryland 20742,
United States
| | - Jerome Baudry
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Nitin Jain
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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