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Alvarez G, Le T, Wong N, Echave J, Pochapsky TC, Asciutto EK. Hydroxylation Regiochemistry Is Robust to Active Site Mutations in Cytochrome P450 cam (CYP101A1). Biochemistry 2022; 61:1790-1800. [PMID: 35960510 PMCID: PMC9721313 DOI: 10.1021/acs.biochem.2c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the hydroxylation of d-camphor by molecular oxygen. The enzyme-catalyzed hydroxylation exhibits a high degree of regioselectivity and stereoselectivity, with a single major product, d-5-exo-hydroxycamphor, suggesting that the substrate is oriented to facilitate this specificity. In previous work, we used an elastic network model and perturbation response scanning to show that normal deformation modes of the enzyme structure are highly responsive not only to the presence of a substrate but also to the substrate orientation. This work examines the effects of mutations near the active site on substrate localization and orientation. The investigated mutations were designed to promote a change in substrate orientation and/or location that might give rise to different hydroxylation products, while maintaining the same carbon and oxygen atom balances as in the wild type (WT) enzyme. Computational experiments and parallel in vitro site-directed mutations of CYP101A1 were used to examine reaction products and enzyme activity. 1H-15N TROSY-HSQC correlation maps were used to compare the computational results with detectable perturbations in the enzyme structure and dynamics. We found that all of the mutant enzymes retained the same regio- and stereospecificity of hydroxylation as the WT enzyme, with varying degrees of efficiency, which suggests that large portions of the enzyme have been subjected to evolutionary pressure to arrive at the appropriate sequence-structure combination for efficient 5-exo hydroxylation of camphor.
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Affiliation(s)
- Guadalupe Alvarez
- Instituto de Ciencias Físicas, Universidad Nacional de San Martín & CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires 1650, Argentina
| | - Thu Le
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Nathan Wong
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Julian Echave
- Instituto de Ciencias Físicas, Universidad Nacional de San Martín & CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires 1650, Argentina
| | - Thomas C Pochapsky
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States.,Department of Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Eliana K Asciutto
- Instituto de Ciencias Físicas, Universidad Nacional de San Martín & CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires 1650, Argentina
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2
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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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3
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Shadrina MS, English AM, Peslherbe GH. Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study. J Chem Theory Comput 2016; 12:2038-46. [PMID: 26938707 DOI: 10.1021/acs.jctc.5b01132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Standard molecular dynamics (MD) simulations of gas diffusion consume considerable computational time and resources even for small proteins. To combat this, temperature-controlled locally enhanced sampling (TLES) examines multiple diffusion trajectories per simulation by accommodating multiple noninteracting copies of a gas molecule that diffuse independently, while the protein and water molecules experience an average interaction from all copies. Furthermore, gas migration within a protein matrix can be accelerated without altering protein dynamics by increasing the effective temperature of the TLES copies. These features of TLES enable rapid simulations of gas diffusion within a protein matrix at significantly reduced (∼98%) computational cost. However, the results of TLES and standard MD simulations have not been systematically compared, which limits the adoption of the TLES approach. We address this drawback here by benchmarking TLES against standard MD in the simulation of O2 diffusion in myoglobin (Mb) as a case study since this model system has been extensively characterized. We find that 2 ns TLES and 108 ns standard simulations map the same network of diffusion tunnels in Mb and uncover the same docking sites, barriers, and escape portals. We further discuss the influence of simulation time as well as the number of independent simulations on the O2 population density within the diffusion tunnels and on the sampling of Mb's conformational space as revealed by principal component analysis. Overall, our comprehensive benchmarking reveals that TLES is an appropriate and robust tool for the rapid mapping of gas diffusion in proteins when the kinetic data provided by standard MD are not required. Furthermore, TLES provides explicit ligand diffusion pathways, unlike most rapid methods.
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Affiliation(s)
- Maria S Shadrina
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
| | - Ann M English
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
| | - Gilles H Peslherbe
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
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4
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Shadrina MS, Peslherbe GH, English AM. Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin’s Gas Diffusion Tunnels. Biochemistry 2015; 54:5268-78. [DOI: 10.1021/acs.biochem.5b00368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria S. Shadrina
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Gilles H. Peslherbe
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Ann M. English
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
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Structural dynamics of the cell wall precursor lipid II in the presence and absence of the lantibiotic nisin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3061-8. [PMID: 25128154 DOI: 10.1016/j.bbamem.2014.07.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 01/06/2023]
Abstract
Representing a physiological "Achilles' heel", the cell wall precursor lipid II (LII) is a prime target for various classes of antibiotics. Over the years LII-binding agents have been recognized as promising candidates and templates in the search for new antibacterial compounds to complement or replace existing drugs. To elucidate the molecular structural basis underlying LII functional mechanism and to better understand if and how lantibiotic binding alters the molecular behavior of LII, we performed molecular dynamics (MD) simulations of phospholipid membrane-embedded LII in the absence and presence of the LII-binding lantibiotic nisin. In a series of 2×4 independent, unbiased 100ns MD simulations we sampled the conformational dynamics of nine LII as well as nine LII-nisin complexes embedded in an aqueous 150mM NaCl/POPC phospholipid membrane environment. We found that nisin binding to LII induces a reduction of LII mobility and flexibility, an outward shift of the LII pentapeptide, an inward movement of the LII disaccharide section, and an overall deeper insertion of the LII tail group into the membrane. The latter effect might indicate an initial step in adopting a stabilizing, scaffold-like structure in the process of nisin-induced membrane leakage. At the same time nisin conformation and LII interaction remain similar to the 1WCO LII-nisin NMR solution structure.
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Shadrina MS, English AM, Peslherbe GH. Effective Simulations of Gas Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O2 Pathways and Escape Routes in T-state Deoxyhemoglobin. J Am Chem Soc 2012; 134:11177-84. [DOI: 10.1021/ja300903c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria S. Shadrina
- Department
of Chemistry and Biochemistry and Centre
for Research in Molecular Modeling, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
| | - Ann M. English
- Department
of Chemistry and Biochemistry and Centre
for Research in Molecular Modeling, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
| | - Gilles H. Peslherbe
- Department
of Chemistry and Biochemistry and Centre
for Research in Molecular Modeling, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
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Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC. Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model 2012; 52:617-48. [PMID: 22339582 PMCID: PMC3317594 DOI: 10.1021/ci200542m] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Metabolism of xenobiotics remains a central challenge
for the discovery
and development of drugs, cosmetics, nutritional supplements, and
agrochemicals. Metabolic transformations are frequently related to
the incidence of toxic effects that may result from the emergence
of reactive species, the systemic accumulation of metabolites, or
by induction of metabolic pathways. Experimental investigation of
the metabolism of small organic molecules is particularly resource
demanding; hence, computational methods are of considerable interest
to complement experimental approaches. This review provides a broad
overview of structure- and ligand-based computational methods for
the prediction of xenobiotic metabolism. Current computational approaches
to address xenobiotic metabolism are discussed from three major perspectives:
(i) prediction of sites of metabolism (SOMs), (ii) elucidation of
potential metabolites and their chemical structures, and (iii) prediction
of direct and indirect effects of xenobiotics on metabolizing enzymes,
where the focus is on the cytochrome P450 (CYP) superfamily of enzymes,
the cardinal xenobiotics metabolizing enzymes. For each of these domains,
a variety of approaches and their applications are systematically
reviewed, including expert systems, data mining approaches, quantitative
structure–activity relationships (QSARs), and machine learning-based
methods, pharmacophore-based algorithms, shape-focused techniques,
molecular interaction fields (MIFs), reactivity-focused techniques,
protein–ligand docking, molecular dynamics (MD) simulations,
and combinations of methods. Predictive metabolism is a developing
area, and there is still enormous potential for improvement. However,
it is clear that the combination of rapidly increasing amounts of
available ligand- and structure-related experimental data (in particular,
quantitative data) with novel and diverse simulation and modeling
approaches is accelerating the development of effective tools for
prediction of in vivo metabolism, which is reflected by the diverse
and comprehensive data sources and methods for metabolism prediction
reviewed here. This review attempts to survey the range and scope
of computational methods applied to metabolism prediction and also
to compare and contrast their applicability and performance.
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Affiliation(s)
- Johannes Kirchmair
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
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Raunest M, Kandt C. Locked on one side only: ground state dynamics of the outer membrane efflux duct TolC. Biochemistry 2012; 51:1719-29. [PMID: 22313049 DOI: 10.1021/bi201814s] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Playing a major role in the expulsion of antibiotics and the secretion of cell toxins in conjunction with inner membrane transporters of three protein superfamilies, the outer membrane channel TolC occurs in at least two states blocking or permitting the passage of substrates. The details of the underlying gating mechanism are not fully understood. Addressing the questions of extracellular access control and periplasmic gating mechanism, we conducted a series of independent, unbiased 150-300 ns molecular dynamics simulations of wild-type TolC in a phospholipid membrane/150 mM NaCl water environment. We find that TolC opens and closes freely on the extracellular side, suggesting the absence of a gating mechanism on this side in the isolated protein. On the periplasmic side, we observe the outer periplasmic bottleneck region adopting in all simulations a conformation more open than the TolC wild-type crystal structures until in one run the successive binding of two sodium ions induces the transition to a conformation more closed than any of the available TolC X-ray structures. Concurrent with a heightened sodium residence probability near Asp374, the inner periplasmic bottleneck region at Asp374 remains closed throughout the simulations unless all NaCl is removed from the system, inducing a reopening of the outer and inner bottleneck. Our findings suggest that TolC is locked only on the periplasmic side in a sodium-dependent manner.
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Affiliation(s)
- Martin Raunest
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life and Medical Sciences Center, University of Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany
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Oloo EO, Kandt C, O'Mara ML, Tieleman DP. Computer simulations of ABC transporter componentsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease. Biochem Cell Biol 2006; 84:900-11. [PMID: 17215877 DOI: 10.1139/o06-182] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Current computer simulation techniques provide robust tools for studying the detailed structure and functional dynamics of proteins, as well as their interaction with each other and with other biomolecules. In this minireview, we provide an illustration of recent progress and future challenges in computer modeling by discussing computational studies of ATP-binding cassette (ABC) transporters. ABC transporters have multiple components that work in a well coordinated fashion to enable active transport across membranes. The mechanism by which members of this superfamily execute transport remains largely unknown. Molecular dynamics simulations initiated from high-resolution crystal structures of several ABC transporters have proven to be useful in the investigation of the nature of conformational coupling events that may drive transport. In addition, fruitful efforts have been made to predict unknown structures of medically relevant ABC transporters, such as P-glycoprotein, using homology-based computational methods. The various techniques described here are also applicable to gaining an atomically detailed understanding of the functional mechanisms of proteins in general.
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Affiliation(s)
- Eliud O Oloo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
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10
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Adcock SA, McCammon JA. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 2006; 106:1589-615. [PMID: 16683746 PMCID: PMC2547409 DOI: 10.1021/cr040426m] [Citation(s) in RCA: 757] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Stewart A. Adcock
- NSF Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0365
| | - J. Andrew McCammon
- NSF Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0365
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11
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Van Roon A, Parsons JR, Govers HAJ. Cytochrome P450cam-monoterpene interactions. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2005; 16:369-84. [PMID: 16234177 DOI: 10.1080/10659360500204533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The use of the molecular mechanics AMBER force field (FF) to predict product profiles for the hydroxylation of the monoterpenes 1R-camphor, 1S-camphor, 1R-norcamphor, 1S-norcamphor and camphane by the enzyme cytochrome P450cam from the soil bacterium Pseudomonas putida was investigated. Predictions were carried out by applying multiple substrate (starting) orientations in the enzyme pocket in two procedures: a procedure based on molecular dynamics (MD) and a procedure based on short MD simulations followed by geometry optimisations. The latter (GO) procedure is faster and enabled the use of more monoterpene starting orientations. Monoterpene orientations were transformed into product profiles by applying both energetic and geometrical criteria appropriate for the (monoterpene) hydrogen abstraction reaction. Good predictions compared to experimental data were obtained for most compounds in both the MD and GO procedures. Prior to the product profile calculations, the FF was calibrated by reproducing the experimental data for the binding energy of 1R-camphor and 1S-camphor to P450cam and the energy of vaporisation of water. Focus of the calibration was on the value for the scaling factor for the electrostatic interactions.
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Affiliation(s)
- A Van Roon
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Earth Surface Processes and Materials, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.
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Shaik S, Kumar D, de Visser SP, Altun A, Thiel W. Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes. Chem Rev 2005; 105:2279-328. [PMID: 15941215 DOI: 10.1021/cr030722j] [Citation(s) in RCA: 964] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sason Shaik
- Department of Organic Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Israel.
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Hays AMA, Dunn AR, Chiu R, Gray HB, Stout CD, Goodin DB. Conformational States of Cytochrome P450cam Revealed by Trapping of Synthetic Molecular Wires. J Mol Biol 2004; 344:455-69. [PMID: 15522298 DOI: 10.1016/j.jmb.2004.09.046] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 09/17/2004] [Accepted: 09/20/2004] [Indexed: 11/15/2022]
Abstract
Members of the ubiquitous cytochrome P450 family catalyze a vast range of biologically significant reactions in mammals, plants, fungi, and bacteria. Some P450s display a remarkable promiscuity in substrate recognition, while others are very specific with respect to substrate binding or regio and stereo-selective catalysis. Recent results have suggested that conformational flexibility in the substrate access channel of many P450s may play an important role in controlling these effects. Here, we report the X-ray crystal structures at 1.8A and 1.5A of cytochrome P450cam complexed with two synthetic molecular wires, D-4-Ad and D-8-Ad, consisting of a dansyl fluorophore linked to an adamantyl substrate analog via an alpha,omega-diaminoalkane chain of varying length. Both wires bind with the adamantyl moiety in similar positions at the camphor-binding site. However, each wire induces a distinct conformational response in the protein that differs from the camphor-bound structure. The changes involve significant movements of the F, G, and I helices, allowing the substrate access channel to adapt to the variable length of the probe. Wire-induced opening of the substrate channel also alters the I helix bulge and Thr252 at the active site with binding of water that has been proposed to assist in peroxy bond cleavage. The structures suggest that the coupling of substrate-induced conformational changes to active-site residues may be different in P450cam and recently described mammalian P450 structures. The wire-induced changes may be representative of the conformational intermediates that must exist transiently during substrate entry and product egress, providing a view of how substrates enter the deeply buried active site. They also support observed examples of conformational plasticity that are believed be responsible for the promiscuity of drug metabolizing P450s. Observation of such large changes in P450cam suggests that substrate channel plasticity is a general property inherent to all P450 structures.
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Affiliation(s)
- Anna-Maria A Hays
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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14
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Tai K. Conformational sampling for the impatient. Biophys Chem 2004; 107:213-20. [PMID: 14967236 DOI: 10.1016/j.bpc.2003.09.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2003] [Revised: 09/20/2003] [Accepted: 09/22/2003] [Indexed: 10/26/2022]
Abstract
Several new methods for sampling conformations of biomolecules have appeared recently. A brief review thereof is presented, with particular emphasis on applications that have been published, and suitability for different kinds of systems. Four methods (namely: RESPA, replica-exchange molecular dynamics, CONCOORD and Gaussian network method) are readily applicable for biomolecular systems.
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Affiliation(s)
- Kaihsu Tai
- Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK.
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15
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Taylor RD, Jewsbury PJ, Essex JW. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. J Comput Chem 2003; 24:1637-56. [PMID: 12926007 DOI: 10.1002/jcc.10295] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The docking of flexible small molecule ligands to large flexible protein targets is addressed in this article using a two-stage simulation-based method. The methodology presented is a hybrid approach where the first component is a dock of the ligand to the protein binding site, based on deriving sets of simultaneously satisfied intermolecular hydrogen bonds using graph theory and a recursive distance geometry algorithm. The output structures are reduced in number by cluster analysis based on distance similarities. These structures are submitted to a modified Monte Carlo algorithm using the AMBER-AA molecular mechanics force field with the Generalized Born/Surface Area (GB/SA) continuum model. This solvent model is not only less expensive than an explicit representation, but also yields increased sampling. Sampling is also increased using a rotamer library to direct some of the protein side-chain movements along with large dihedral moves. Finally, a softening function for the nonbonded force field terms is used, enabling the potential energy function to be slowly turned on throughout the course of the simulation. The docking procedure is optimized, and the results are presented for a single complex of the arabinose binding protein. It was found that for a rigid receptor model, the X-ray binding geometry was reproduced and uniquely identified based on the associated potential energy. However, when side-chain flexibility was included, although the X-ray structure was identified, it was one of three possible binding geometries that were energetically indistinguishable. These results suggest that on relaxing the constraint on receptor flexibility, the docking energy hypersurface changes from being funnel-like to rugged. A further 14 complexes were then examined using the optimized protocol. For each complex the docking methodology was tested for a fully flexible ligand, both with and without protein side-chain flexibility. For the rigid protein docking, 13 out of the 15 test cases were able to find the experimental binding mode; this number was reduced to 11 for the flexible protein docking. However, of these 11, in the majority of cases the experimental binding mode was not uniquely identified, but was present in a cluster of low energy structures that were energetically indistinguishable. These results not only support the presence of a rugged docking energy hypersurface, but also suggest that it may be necessary to consider the possibility of more than one binding conformation during ligand optimization.
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Affiliation(s)
- Richard D Taylor
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
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Jung C, Bec N, Lange R. Substrates modulate the rate-determining step for CO binding in cytochrome P450cam (CYP101). A high-pressure stopped-flow study. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:2989-96. [PMID: 12071963 DOI: 10.1046/j.1432-1033.2002.02980.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The high-pressure stopped-flow technique is applied to study the CO binding in cytochrome P450cam (P450cam) bound with homologous substrates (1R-camphor, camphane, norcamphor and norbornane) and in the substrate-free protein. The activation volume DeltaV # of the CO on-rate is positive for P450cam bound with substrates that do not contain methyl groups. The kon rate constant for these substrate complexes is in the order of 3 x 10(6) M(-1) x s(-1). In contrast, P450cam complexed with substrates carrying methyl groups show a negative activation volume and a low kon rate constant of approximately 3 x 10(4) M(-1) x s(-1). By relating kon and DeltaV # with values for the compressibility and the influx rate of water for the heme pocket of the substrate complexes it is concluded that the positive activation volume is indicative for a loosely bound substrate that guarantees a high solvent accessibility for the heme pocket and a very compressible active site. In addition, subconformers have been found for the substrate-free and camphane-bound protein which show different CO binding kinetics.
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Affiliation(s)
- Christiane Jung
- Max-Delbrück-Center for Molecular Medicine, Protein Dynamics Laboratory, Berlin, Germany.
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17
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Lill MA, Helms V. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD). J Chem Phys 2001. [DOI: 10.1063/1.1407293] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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