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Giovannelli E, Cardini G, Gellini C, Pietraperzia G, Chelli R. Computing Free Energy Differences of Configurational Basins. J Chem Theory Comput 2015; 11:3561-71. [DOI: 10.1021/acs.jctc.5b00248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Edoardo Giovannelli
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Cristina Gellini
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Giangaetano Pietraperzia
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Riccardo Chelli
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
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2
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Brownian dynamics simulation of peptides with the University of Houston Brownian Dynamics (UHBD) program. Methods Mol Biol 2015. [PMID: 25555722 DOI: 10.1007/978-1-4939-2285-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum relaxation time. On the other hand, it is faster than molecular dynamics by approximating the solvent by a continuum and by operating in the over-damped limit. This chapter introduces the use of the University of Houston Brownian Dynamics (UHBD) program [1, 2] to perform Brownian dynamics simulation on peptides.
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3
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Moritsugu K, Kidera A, Smith JC. Solvent Friction Effects Propagate over the Entire Protein Molecule through Low-Frequency Collective Modes. J Phys Chem B 2014; 118:8559-65. [DOI: 10.1021/jp503956m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kei Moritsugu
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Akinori Kidera
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jeremy C. Smith
- Center
for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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4
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Jang H, Arce FT, Ramachandran S, Capone R, Lal R, Nussinov R. β-Barrel topology of Alzheimer's β-amyloid ion channels. J Mol Biol 2010; 404:917-34. [PMID: 20970427 PMCID: PMC7291702 DOI: 10.1016/j.jmb.2010.10.025] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 10/06/2010] [Accepted: 10/15/2010] [Indexed: 11/19/2022]
Abstract
Emerging evidence supports the ion channel mechanism for Alzheimer's disease pathophysiology wherein small β-amyloid (Aβ) oligomers insert into the cell membrane, forming toxic ion channels and destabilizing the cellular ionic homeostasis. Solid-state NMR-based data of amyloid oligomers in solution indicate that they consist of a double-layered β-sheets where each monomer folds into β-strand-turn-β-strand and the monomers are stacked atop each other. In the membrane, Aβ peptides are proposed to be β-type structures. Experimental structural data available from atomic force microscopy (AFM) imaging of Aβ oligomers in membranes reveal heterogeneous channel morphologies. Previously, we modeled the channels in a non-tilted organization, parallel with the cross-membrane normal. Here, we modeled a β-barrel-like organization. β-Barrels are common in transmembrane toxin pores, typically consisting of a monomeric chain forming a pore, organized in a single-layered β-sheet with antiparallel β-strands and a right-handed twist. Our explicit solvent molecular dynamics simulations of a range of channel sizes and polymorphic turns and comparisons of these with AFM image dimensions support a β-barrel channel organization. Different from the transmembrane β-barrels where the monomers are folded into a circular β-sheet with antiparallel β-strands stabilized by the connecting loops, these Aβ barrels consist of multimeric chains forming double β-sheets with parallel β-strands, where the strands of each monomer are connected by a turn. Although the Aβ barrels adopt the right-handed β-sheet twist, the barrels still break into heterogeneous, loosely attached subunits, in good agreement with AFM images and previous modeling. The subunits appear mobile, allowing unregulated, hence toxic, ion flux.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Fernando Teran Arce
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Srinivasan Ramachandran
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo Capone
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ratnesh Lal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA
- Department of Human Molecular Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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5
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Zhong L, Matthews JF, Hansen PI, Crowley MF, Cleary JM, Walker RC, Nimlos MR, Brooks CL, Adney WS, Himmel ME, Brady JW. Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Ibeta: the enzyme-substrate complex. Carbohydr Res 2009; 344:1984-92. [PMID: 19699474 DOI: 10.1016/j.carres.2009.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2008] [Revised: 07/13/2009] [Accepted: 07/14/2009] [Indexed: 11/29/2022]
Abstract
Cellobiohydrolases are the dominant components of the commercially relevant Trichoderma reesei cellulase system. Although natural cellulases can totally hydrolyze crystalline cellulose to soluble sugars, the current enzyme loadings and long digestion times required render these enzymes less than cost effective for biomass conversion processes. It is clear that cellobiohydrolases must be improved via protein engineering to reduce processing costs. To better understand cellobiohydrolase function, new simulations have been conducted using charmm of cellobiohydrolase I (CBH I) from T.reesei interacting with a model segment (cellodextrin) of a cellulose microfibril in which one chain from the substrate has been placed into the active site tunnel mimicking the hypothesized configuration prior to final substrate docking (i.e., the +1 and +2 sites are unoccupied), which is also the structure following a catalytic bond scission. No tendency was found for the protein to dissociate from or translate along the substrate surface during this initial simulation, nor to align with the direction of the cellulose chains. However, a tendency for the decrystallized cellodextrin to partially re-anneal into the cellulose surface hints that the arbitrary starting configuration selected was not ideal.
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Affiliation(s)
- Linghao Zhong
- Department of Food Science, Cornell University, Ithaca, NY 14853, United States
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6
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Jang H, Michaud-Agrawal N, Johnston JM, Woolf TB. How to lose a kink and gain a helix: pH independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers. Proteins 2008; 72:299-312. [PMID: 18214961 DOI: 10.1002/prot.21925] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have simulated two conformations of the fusion domain of influenza hemagglutinin (HA) within explicit water, salt, and heterogeneous lipid bilayers composed of POPC:POPG (4:1). Each conformation has seven different starting points in which the initial peptide structure is the same for each conformation, but the location across the membrane normal and lipid arrangement around the peptide are varied, giving a combined total simulation time of 140 ns. For the HA5 conformation (primary structure from recent NMR spectroscopy at pH = 5), the peptide exhibits a stable and less kinked structure in the lipid bilayer compared to that from the NMR studies. The relative fusogenic behavior of the different conformations has been investigated by calculation of the relative free energy of insertion into the hydrophobic region of lipid bilayer as a function of the depth of immersion. For the HA7 conformations (primary structure from recent NMR spectroscopy at pH = 7.4), while the N-terminal helix preserves its initial structure, the flexible C-terminal chain produces a transient helical motif inside the lipid bilayer. This conformational change is pH-independent, and is closely related to the peptide insertion into the lipid bilayer.
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Affiliation(s)
- Hyunbum Jang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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7
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Hamelberg D, Shen T, McCammon JA. Insight into the role of hydration on protein dynamics. J Chem Phys 2007; 125:094905. [PMID: 16965117 DOI: 10.1063/1.2232131] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The potential energy surface of a protein is rough. This intrinsic energetic roughness affects diffusion, and hence the kinetics. The dynamics of a system undergoing Brownian motion on this surface in an implicit continuum solvent simulation can be tuned via the frictional drag or collision frequency to be comparable to that of experiments or explicit solvent simulations. We show that the kinetic rate constant for a local rotational isomerization in stochastic simulations with continuum solvent and a collision frequency of 2 ps(-1) is about 10(4) times faster than that in explicit water and experiments. A further increase in the collision frequency to 60 ps(-1) slows down the dynamics, but does not fully compensate for the lack of explicit water. We also show that the addition of explicit water does not only slow down the dynamics by increasing the frictional drag, but also increases the local energetic roughness of the energy landscape by as much as 1.0 kcal/mol.
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Affiliation(s)
- Donald Hamelberg
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA.
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8
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Nina M, Im W, Roux B. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophys Chem 2007; 78:89-96. [PMID: 17030305 DOI: 10.1016/s0301-4622(98)00236-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/1998] [Revised: 12/02/1998] [Accepted: 12/03/1998] [Indexed: 10/18/2022]
Abstract
Recently, we presented a Green's function approach for the calculation of analytic continuum electrostatic solvation forces based on numerical solutions of the finite-difference Poisson-Botzmann (FDPB) equation [Im et al., Comp. Phys. Comm. 111 (1998) 59]. In this treatment the analytic forces were explicitly defined as the first derivative of the FDPB continuum electrostatic free energy with respect to the coordinates of the solute atoms. A smooth intermediate region for the solute-solvent dielectric boundary needed to be introduced to avoid abrupt discontinuous variations in the solvation free energy and forces as a function of the atomic positions. In the present paper we extend the set of optimized radii, which was previously parametrized from molecular dynamics free energy simulations of the 20 standard amino acids with explicit solvent molecules [Nina et al., J. Phys. Chem. 101 (1997) 5239], to yield accurate solvation free energy by taking the influence of the smoothed dielectric region into account.
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Affiliation(s)
- M Nina
- Department of Physics, Université de Montréal, C.P. 6128, succ. Centre-Ville, Montréal, QC, Canada H3C 3J7
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9
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Mijajlovic M, Biggs MJ. On Use of the Amber Potential with the Langevin Dipole Method. J Phys Chem B 2007; 111:7591-602. [PMID: 17550281 DOI: 10.1021/jp0701744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Inclusion of solvent effects in biomolecular simulations is most ideally done using explicit methods, as they are able to capture the heterogeneous environment typical of biomolecules and systems involving them (e.g., proteins at solid interfaces). Common explicit methods based on molecular solvent models (e.g., TIP and SPC models) and molecular dynamic or Monte Carlo simulation are computationally expensive and are, therefore, not well-suited to situations where many simulations are required (e.g., in the ab initio structure prediction or design contexts). In such cases, more coarse-grained explicit approaches such as the Langevin dipole (LD) method of Warshel and co-workers are more appropriate. The recent incarnations of the LD method appear to produce good solvation free energy estimates. These incarnations use charges and solute structures obtained from high-level quantum mechanics simulations. As such an approach is clearly not possible for larger solutes or when many structures are to be considered, an alternative must be sought. One possibility is to use structures and charges derived from an existing analytical potential model-we report on such a coupling here with the Amber potential model. The accuracy and computational performance of this hybrid approach, which we term LD-Amber to distinguish it from previous incarnations of the LD method, was assessed by comparing results obtained from the approach with those from experiment and other theoretical methods for the solvation of 18 amino acid analogues and the alanine dipeptide. This comparison shows that the LD-Amber approach can yield results in line with experiment both qualitatively and quantitatively and is as accurate as other explicit methods while being computationally much cheaper.
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Affiliation(s)
- Milan Mijajlovic
- Institute for Materials and Processes, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, United Kingdom
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10
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Abstract
The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis-trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C(7) hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the alpha-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis-trans isomerization increases. It is found that the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about the non-prolyl and prolyl peptide bonds in both the gas phase and the solutions. The pertinent distance d(N...H-N(NHMe)) can successfully describe the increase in the rotational barriers for the non-prolyl and prolyl trans-cis isomerization as the solvent polarity increases and the higher barriers for the non-prolyl residue than for the prolyl residue, as seen in experimental and calculated results. By analysis of the contributions to rotational barriers, the cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. The calculated cis populations and rotational barriers to the cis-trans isomerization for both the dipeptides in chloroform and/or water accord with the experimental values.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry and Basic Science Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea.
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11
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Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci U S A 2006; 103:8331-6. [PMID: 16709675 PMCID: PMC1482494 DOI: 10.1073/pnas.0600118103] [Citation(s) in RCA: 226] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks-Chandler-Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces.
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Affiliation(s)
| | - Nathan A. Baker
- Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University, 700 South Euclid Avenue, Campus Box 8036, St. Louis, MO 63110
- To whom correspondence should be addressed. E-mail:
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12
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Jang H, Woolf TB. Multiple pathways in conformational transitions of the alanine dipeptide: An application of dynamic importance sampling. J Comput Chem 2006; 27:1136-41. [PMID: 16721720 DOI: 10.1002/jcc.20444] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We present multiple dynamic transition pathways on the two-dimensional dihedral plane between conformational states of the alanine dipeptide. The method used in this study is dynamic importance sampling (DIMS). To perform DIMS, unbiased molecular dynamic simulations are used to generate equilibrium ensembles for the alanine dipeptide within different states. Free energy surfaces on the dihedral plane are calculated from the equilibrium simulations, and four energy minima defined from the surface are used as the starting and ending points for DIMS dynamics. The DIMS method represents an important step towards finding multiple transition pathways within complex biomolecular systems.
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Affiliation(s)
- Hyunbum Jang
- Department of Physiology, Johns Hopkins University, Baltimore, Maryland 21205, USA.
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13
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Fleming PJ, Fitzkee NC, Mezei M, Srinivasan R, Rose GD. A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA). Protein Sci 2004; 14:111-8. [PMID: 15576559 PMCID: PMC2253334 DOI: 10.1110/ps.041047005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In aqueous solution, the ensemble of conformations sampled by peptides and unfolded proteins is largely determined by their interaction with water. It has been a long-standing goal to capture these solute-water energetics accurately and efficiently in calculations. Historically, accessible surface area (ASA) has been used to estimate these energies, but this method breaks down when applied to amphipathic peptides and proteins. Here we introduce a novel method in which hydrophobic ASA is determined after first positioning water oxygens in hydrogen-bonded orientations proximate to all accessible peptide/protein backbone N and O atoms. This conditional hydrophobic accessible surface area is termed CHASA. The CHASA method was validated by predicting the polyproline-II (P(II)) and beta-strand conformational preferences of non-proline residues in the coil library (i.e., non-alpha-helix, non-beta-strand, non-beta-turn library derived from X-ray elucidated structures). Further, the method successfully rationalizes the previously unexplained solvation energies in polyalanyl peptides and compares favorably with published experimentally determined P(II) residue propensities. We dedicate this paper to Frederic M. Richards.
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Affiliation(s)
- Patrick J Fleming
- Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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14
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Drozdov AN, Grossfield A, Pappu RV. Role of solvent in determining conformational preferences of alanine dipeptide in water. J Am Chem Soc 2004; 126:2574-81. [PMID: 14982467 DOI: 10.1021/ja039051x] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Evidence from a variety of spectroscopic probes indicates that (phi, psi) values corresponding to the left-handed polyproline II helix (P(II)) are preferred for short alanine-based peptides in water. On the basis of results from theoretical studies, it is believed that the observed preference is dictated by favorable peptide-solvent interactions, which are realized through formation of optimal hydrogen-bonding water bridges between peptide donor and acceptor groups. In the present study, we address this issue explicitly by analyzing the hydration structure and thermodynamics of 16 low-energy conformers of the alanine dipeptide (N-acetylalanine-N'-methylamide) in liquid water. Monte Carlo simulations in the canonical ensemble were performed under ambient conditions with all-atom OPLS parameters for the alanine dipeptide and the TIP5P model for water. We find that the number of hydrogen-bonded water molecules connecting the peptide group donor and acceptor atoms has no effect on the solvation thermodynamics. Instead, the latter are determined by the work done to fully hydrate the peptide. This work is minimal for conformations that are characterized by a minimal overlap of the primary hydration shells around the peptide donor and acceptor atoms. As a result, peptide-solvent interactions favor "compact" conformations that do not include P(II)-like geometries. Our main conclusion is that the experimentally observed preference for P(II) does not arise due to favorable direct interactions between the peptide and water molecules. Instead, the latter act to unmask underlying conformational preferences that are a consequence of minimizing intrapeptide steric conflicts.
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Affiliation(s)
- Alexander N Drozdov
- Department of Biomedical Engineering, Washington University in St. Louis, Campus Box 1097, St. Louis, Missouri 63130, USA
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15
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Affiliation(s)
- Nathan A Baker
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, USA
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16
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Abstract
Helix-capping motifs are believed to play an important role in stabilizing alpha-helices and defining helix start and stop signals. We performed microsecond scale Brownian dynamics simulations to study ten XAAD sequences, with X = (A,E,I,L,N,Q,S,T,V,Y), to examine their propensity to form helix capping motifs and correlate these results with those obtained from analyzing a structural database of proteins. For the widely studied capping box motif S**D, where the asterisk can be any amino acid residue, the simulations suggested that one of the two hydrogen bonds proposed earlier as a stabilizing factor might not be as important. On the other hand, side-chain interactions between the capping residue and the third residue downstream on the polypeptide chain might also play a role in stabilizing this motif. These results are consistent with explicit-solvent molecular dynamics simulations of two capping box motifs found in the proteins BPTI and alpha-dendrotoxin. Principal component analysis of the SAAD trajectory showed that the first three principal components, after those corresponding to translational-rotational motion were removed, accounted for more than half of the conformational fluctuations. The first component separated the conformational space into two parts with the all-helical conformation and the capping box motif lying largely in one part. The second component, on the other hand, could be used to describe conformational transitions between the all-helical form and the capping box motif.
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Affiliation(s)
- Tongye Shen
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0365, USA.
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17
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Fogolari F, Brigo A, Molinari H. Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys J 2003; 85:159-66. [PMID: 12829472 PMCID: PMC1303073 DOI: 10.1016/s0006-3495(03)74462-2] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2002] [Accepted: 03/10/2003] [Indexed: 11/30/2022] Open
Abstract
Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poisson-Boltzmann equation has been very seldom used to obtain solvation forces for molecular dynamics simulation. We propose here a fast and reliable methodology to implement continuum forces in standard molecular mechanics and dynamics algorithms. Results for a totally unrestrained 1 ns molecular dynamics simulation of a small protein are quantitatively similar to results obtained by explicit solvent molecular dynamics simulations.
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Affiliation(s)
- Federico Fogolari
- Dipartimento Scientifico e Tecnologico, Università di Verona, 37134 Verona, Italy.
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18
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Król M. Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer. J Comput Chem 2003; 24:531-46. [PMID: 12632469 DOI: 10.1002/jcc.10186] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The present study tests performance of different solvation models applied to molecular dynamics simulation of a large, dimeric protein molecule. Analytical Continuum Electrostatics (ACE) with two different parameter sets, older V98 and new V01, and Effective Energy Function (EEF) are employed in molecular dynamics simulation of immunoglobulin G (IgG) light chain dimer and variable domain of IgG light chain. Results are compared with explicit solvent and distance dependent dielectric constant (DDE) calculations. The overall analysis shows that the EEF method yields results comparable to explicit solvent simulations; however, the stability of simulations is lower. On the other hand, the ACE_V98 model does not seem to achieve the accuracy or stability expected in nanosecond timescale MD simulation for the studied systems. The ACE_V01 model greatly improves stability of the calculation; nonetheless, changes in radius of gyration and solvent accessible surface of the studied systems may indicate that the parameter set still needs to be improved if the method is supposed to be used for simulations of large, polymeric proteins. Additionally, electrostatic contribution to the solvation free energy calculated in the ACE model is compared with a numerical treatment of the dielectric continuum model. Wall clock time of all simulations is compared. It shows that EEF calculation is six times faster than corresponding ACE and 50 times faster than explicit solvent simulations.
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Affiliation(s)
- Marcin Król
- Department of Biostatistics and Medical Informatics Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Kraków, Poland.
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19
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Weise CF, Weisshaar JC. Conformational Analysis of Alanine Dipeptide from Dipolar Couplings in a Water-Based Liquid Crystal. J Phys Chem B 2003. [DOI: 10.1021/jp026854i] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph F. Weise
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1396
| | - James C. Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1396
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20
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Andricioaei I, Dinner AR, Karplus M. Self-guided enhanced sampling methods for thermodynamic averages. J Chem Phys 2003. [DOI: 10.1063/1.1528893] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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21
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Cui Q, Smith VH. Solvation structure, thermodynamics, and conformational dependence of alanine dipeptide in aqueous solution analyzed with reference interaction site model theory. J Chem Phys 2003. [DOI: 10.1063/1.1524617] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Fogolari F, Brigo A, Molinari H. The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recognit 2002; 15:377-92. [PMID: 12501158 DOI: 10.1002/jmr.577] [Citation(s) in RCA: 301] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. The Poisson-Boltzmann equation constitutes one of the most fundamental approaches to treat electrostatic effects in solution. The theoretical basis of the Poisson-Boltzmann equation is reviewed and a wide range of applications is presented, including the computation of the electrostatic potential at the solvent-accessible molecular surface, the computation of encounter rates between molecules in solution, the computation of the free energy of association and its salt dependence, the study of pKa shifts and the combination with classical molecular mechanics and dynamics. Theoretical results may be used for rationalizing or predicting experimental results, or for suggesting working hypotheses. An ever-increasing body of successful applications proves that the Poisson-Boltzmann equation is a useful tool for structural biology and complementary to other established experimental and theoretical methodologies.
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Affiliation(s)
- F Fogolari
- Dipartimento Scientifico Tecnologico, Università degli Studi di Verona, Cá Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy.
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23
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Lu BZ, Chen WZ, Wang CX, Xu XJ. Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation. Proteins 2002; 48:497-504. [PMID: 12112674 DOI: 10.1002/prot.10172] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The electrostatic force including the intramolecular Coulombic interactions and the electrostatic contribution of solvation effect were entirely calculated by using the finite difference Poisson-Boltzmann method (FDPB), which was incorporated into the GROMOS96 force field to complete a new finite difference stochastic dynamics procedure (FDSD). Simulations were performed on an insulin dimer. Different relative dielectric constants were successively assigned to the protein interior; a value of 17 was selected as optimal for our system. The simulation data were analyzed and compared with those obtained from 500-ps molecular dynamics (MD) simulation with explicit water and a 500-ps conventional stochastic dynamics (SD) simulation without the mean solvent force. The results indicate that the FDSD method with GROMOS96 force field is suitable to study the dynamics and structure of proteins in solution if used with the optimal protein dielectric constant.
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Affiliation(s)
- Ben Zhuo Lu
- Department of Astronomy and Applied Physics, University of Science and Technology of China, Hefei, China
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24
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Gonçalves PFB, Stassen H. New approach to free energy of solvation applying continuum models to molecular dynamics simulation. J Comput Chem 2002; 23:706-14. [PMID: 11948588 DOI: 10.1002/jcc.10076] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new approach to the calculation of the free energy of solvation from trajectories obtained by molecular dynamics simulation is presented. The free energy of solvation is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent nonpolar (repulsion and dispersion) interactions, and the electrostatic solvation of the solute. The electrostatic term is calculated based on ideas developed for the broadly used continuum models, the cavitational contribution from the excluded volume by the Claverie-Pierotti model, and the Van der Waals term directly from the molecular dynamics simulation. The proposed model is tested for diluted aqueous solutions of simple molecules containing a variety of chemically important functions: methanol, methylamine, water, methanethiol, and dichloromethane. These solutions were treated by molecular dynamics simulations using SPC/E water and the OPLS force field for the organic molecules. Obtained free energies of solvation are in very good agreement with experimental data.
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Affiliation(s)
- Paulo F B Gonçalves
- Grupo de Química Teórica, Instituto de Química, Universidade Federal do Rio Grande do Sul, 91540-000 Porto Alegre- RS, Brazil
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25
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Hassan SA, Mehler EL. A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins. Proteins 2002; 47:45-61. [PMID: 11870864 DOI: 10.1002/prot.10059] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An analysis of the screened Coulomb potential--implicit solvent model (SCP--ISM) is presented showing that general equations for both the electrostatic and solvation free energy can be derived in a continuum approach, using statistical averaging of the polarization field created by the solvent around the molecule. The derivation clearly shows how the concept of boundary, usually found in macroscopic approaches, is eliminated when the continuum model is obtained from a microscopic treatment using appropriate averaging techniques. The model is used to study the alanine dipeptide in aqueous solution, as well as the discrimination of native protein structures from misfolded conformations. For the alanine dipeptide the free energy surface in the phi--psi space is calculated and compared with recently reported results of a detailed molecular dynamics simulation using an explicit representation of the solvent, and with other available data. The study showed that the results obtained using the SCP--ISM are comparable to those of the explicit water calculation and compares favorably to the FDPB approach. Both transition states and energy minima show a high correlation (r > 0.98) with the results obtained in the explicit water analysis. The study of the misfolded structures of proteins comprised the analysis of three standard decoy sets, namely, the EMBL, Park and Levitt, and Baker's CASP3 sets. In all cases the SCP--ISM discriminated well the native structures of the proteins, and the best-predicted structures were always near-native (cRMSD approximately 2 A).
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Affiliation(s)
- Sergio A Hassan
- Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029-6574, USA
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26
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Ferrara P, Apostolakis J, Caflisch A. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins 2002; 46:24-33. [PMID: 11746700 DOI: 10.1002/prot.10001] [Citation(s) in RCA: 226] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A solvation term based on the solvent accessible surface area (SASA) is combined with the CHARMM polar hydrogen force field for the efficient simulation of peptides and small proteins in aqueous solution. Only two atomic solvation parameters are used: one is negative for favoring the direct solvation of polar groups and the other positive for taking into account the hydrophobic effect on apolar groups. To approximate the water screening effects on the intrasolute electrostatic interactions, a distance-dependent dielectric function is used and ionic side chains are neutralized. The use of an analytical approximation of the SASA renders the model extremely efficient (i.e., only about 50% slower than in vacuo simulations). The limitations and range of applicability of the SASA model are assessed by simulations of proteins and structured peptides. For the latter, the present study and results reported elsewhere show that with the SASA model it is possible to sample a significant amount of folding/unfolding transitions, which permit the study of the thermodynamics and kinetics of folding at an atomic level of detail.
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Affiliation(s)
- Philippe Ferrara
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
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27
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Fogolari F, Esposito G, Viglino P, Molinari H. Molecular mechanics and dynamics of biomolecules using a solvent continuum model. J Comput Chem 2001; 22:1830-1842. [PMID: 12116414 DOI: 10.1002/jcc.1134] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830-1842, 2001
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Affiliation(s)
- F. Fogolari
- Dipartimento Scientifico e Tecnologico, Universita' di Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
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28
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Shen T, Wong CF, McCammon JA. Atomistic Brownian dynamics simulation of peptide phosphorylation. J Am Chem Soc 2001; 123:9107-11. [PMID: 11552818 DOI: 10.1021/ja010190t] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the implementation of an all-atom Brownian dynamics simulation model of peptides using the constraint algorithm LINCS. The algorithm has been added as a part of UHBD. It uses adaptive time steps to achieve a balance between computational speed and stability. The algorithm was applied to study the effect of phosphorylation on the conformational preference of the peptide Gly-Ser-Ser-Ser. We find that the middle serine residue experiences considerable conformational change from the C(7eq) to the alpha(R) structure upon phosphorylation. NMR (3)J coupling constants were also computed from the Brownian trajectories using the Karplus equation. The calculated (3)J results agree reasonably well with experimental data for phosphorylated peptide but less so for doubly charged phosphorylated one.
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Affiliation(s)
- T Shen
- Department of Physics, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093-0365, USA.
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29
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Mark P, Nilsson L. Molecular Dynamics Simulations of the Ala-Pro Dipeptide in Water: Conformational Dynamics of Trans and Cis Isomers Using Different Water Models. J Phys Chem B 2001. [DOI: 10.1021/jp0044781] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pekka Mark
- Karolinska Institutet, Department of Bioscience at Novum, S-141 57 Huddinge, Sweden
| | - Lennart Nilsson
- Karolinska Institutet, Department of Bioscience at Novum, S-141 57 Huddinge, Sweden
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30
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Loeffler HH, Sotriffer CA, Winger RH, Liedl KR, Rode BM. Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine. J Comput Chem 2001. [DOI: 10.1002/jcc.1050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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31
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33
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Abstract
A protocol for the rapid energetic analysis of protein-ligand complexes has been developed. This protocol involves the generation of protein-ligand complex ensembles followed by an analysis of the binding free energy components. We apply this methodology toward understanding the origin of binding specificity within the human immunodeficiency virus/feline immunodeficiency virus (HIV/FIV) protease system, a model system for drug resistance studies. A distinct difference in the internal strain of an inhibitor within each protein environment clearly favors the HIV protease complex, as observed experimentally. Our analysis also predicts that residues within the S2-S3 pockets of the FIV protease active site are responsible for this strain. Close examination of the active site residue contributions to interaction energy and desolvation energy identifies specific amino acids that may also play a role in determining the binding preferences of these two enzymes. Proteins 1999;36:318-331.
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Affiliation(s)
- B N Dominy
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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34
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Potter MJ, Kirchhoff PD, Carlson HA, McCammon JA. Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(19990715)20:9<956::aid-jcc7>3.0.co;2-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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35
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Williams DJ, Hall KB. Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model. Biophys J 1999; 76:3192-205. [PMID: 10354444 PMCID: PMC1300288 DOI: 10.1016/s0006-3495(99)77471-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Three unrestrained stochastic dynamics simulations have been carried out on the RNA hairpin GGAC[UUCG] GUCC, using the AMBER94 force field (Cornell et al., 1995. J. Am. Chem. Soc. 117:5179-5197) in MacroModel 5.5 (Mohamadi et al., 1990. J. Comp. Chem. 11:440-467) and either the GB/SA continuum solvation model (Still et al., 1990. J. Am. Chem. Soc. 112:6127-6129) or a linear distance-dependent dielectric (1/R) treatment. The linear distance-dependent treatment results in severe distortion of the nucleic acid structure, restriction of all hydroxyl dihedrals, and collapse of the counterion atmosphere over the course of a 5-ns simulation. An additional vacuum simulation without counterions shows somewhat improved behavior. In contrast, the two GB/SA simulations (1.149 and 3.060 ns in length) give average structures within 1.2 A of the initial NMR structure and in excellent agreement with results of an earlier explicit solvent simulation (Miller and Kollman, 1997. J. Mol. Biol. 270:436-450). In a 3-ns GB/SA simulation starting with the incorrect UUCG tetraloop structure (Cheong et al., 1990. Nature. 346:680-682), this loop conformation converts to the correct loop geometry (Allain and Varani, 1995. J. Mol. Biol. 250:333-353), suggesting enhanced sampling relative to the previous explicit solvent simulation. Thermodynamic effects of 2'-deoxyribose substitutions of loop nucleotides were experimentally determined and are found to correlate with the fraction of time the ribose 2'-OH is hydrogen bonded and the distribution of the hydroxyl dihedral is observed in the GB/SA simulations. The GB/SA simulations thus appear to faithfully represent structural features of the RNA without the computational expense of explicit solvent.
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Affiliation(s)
- D J Williams
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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36
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Colominas C, Luque FJ, Orozco M. Monte Carlo-MST: New strategy for representation of solvent configurational space in solution. J Comput Chem 1999; 20:665-678. [DOI: 10.1002/(sici)1096-987x(199905)20:7<665::aid-jcc2>3.0.co;2-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/1998] [Accepted: 12/07/1998] [Indexed: 11/12/2022]
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37
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Dominy BN, Brooks CL. Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids. J Phys Chem B 1999. [DOI: 10.1021/jp984440c] [Citation(s) in RCA: 327] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian N. Dominy
- Department of Molecular Biology, TPC6, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Charles L. Brooks
- Department of Molecular Biology, TPC6, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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38
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Friedrichs M, Zhou R, Edinger SR, Friesner RA. Poisson−Boltzmann Analytical Gradients for Molecular Modeling Calculations. J Phys Chem B 1999. [DOI: 10.1021/jp982513m] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Abstract
The role of phosphorylation in stabilizing the N-termini of alpha-helices is examined using computer simulations of model peptides. The models comprise either a phosphorylated or unphosphorylated serine at the helix N-terminus, followed by nine alanines. Monte Carlo/stochastic Dynamics simulations were performed on the model helices. The simulations revealed a distinct stabilization of the helical conformation at the N-terminus after phosphorylation. The stabilization was attributable to favorable electrostatic interactions between the phosphate and the helix backbone. However, direct helix capping by the phosphorylated sidechain was not observed. The results of the calculations are consistent with experimental evidence on the stabilization of helices by phosphates and other anions.
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Affiliation(s)
- J L Smart
- Molecular Simulations, Inc., San Diego, CA 92121, USA
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40
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Apostolakis J, Ferrara P, Caflisch A. Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water. J Chem Phys 1999. [DOI: 10.1063/1.477819] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Wu X, Wang S. Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search. J Phys Chem B 1998. [DOI: 10.1021/jp9817372] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiongwu Wu
- Institute for Cognitive and Computational Sciences, Georgetown University Medical Center, The New Research Building, EP07 3970 Reservoir Road, Washington, D.C. 20007
| | - Shaomeng Wang
- Institute for Cognitive and Computational Sciences, Georgetown University Medical Center, The New Research Building, EP07 3970 Reservoir Road, Washington, D.C. 20007
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