51
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Wei NN, Hamza A, Hao C, Johnson-Scalise T, Xiu Z, Naftolin F, Zhan CG. Protein flexibility and conformational states of Leishmania antigen eIF-4A: identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling. J Biomol Struct Dyn 2012; 31:841-53. [PMID: 22963753 DOI: 10.1080/07391102.2012.713781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent homology modeling studies have identified specific residues (epitope) of the Leishmania RNA helicase protein (LmeIF) that stimulates production of IL-12 cytokine. However, question remains concerning how LmeIF's N-terminal moiety initiates adjuvant effects. Extensive molecular modeling combining the normal mode analysis (NMA) and molecular dynamics simulations, in the present study, has demonstrated that the LmeIF structure may exist in two different forms corresponding to the extended and collapsed (closed) states of the entire structure. The computational results showed that the two domains of the LmeIF structure tend to undergo large fluctuations in a concerted fashion and have strong effect on the solvent accessible surface of the epitope situated on the N-terminal structure. The conformational freedom of the C-terminal domains may explain why the entire LmeIF protein is not as active as the N-terminal moiety. Thereafter, a comparative genome analysis with subsequent homology modeling and molecular electrostatic potential (MEP) techniques allowed us to predict a novel and plausible RNA helicase (LI-helicase) from the Listeria source with adjuvant property as observed for the Leishmania eIF-4A protein. The structural folding and MEP maps revealed similar topologies of the epitope of both LmeIF and LI-helicase proteins and striking identity in the local disposition of the charged groups. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:7.
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Affiliation(s)
- Ning-Ning Wei
- Department of Pharmaceutical Sciences , College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA
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52
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Lewis AK, Valley CC, Sachs JN. TNFR1 Signaling Is Associated with Backbone Conformational Changes of Receptor Dimers Consistent with Overactivation in the R92Q TRAPS Mutant. Biochemistry 2012; 51:6545-55. [DOI: 10.1021/bi3006626] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrew K. Lewis
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, Minneapolis,
Minnesota 55455, United States
| | - Christopher C. Valley
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, Minneapolis,
Minnesota 55455, United States
| | - Jonathan N. Sachs
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, Minneapolis,
Minnesota 55455, United States
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53
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Venkatraman V, Ritchie DW. Flexible protein docking refinement using pose-dependent normal mode analysis. Proteins 2012; 80:2262-74. [PMID: 22610423 DOI: 10.1002/prot.24115] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 04/10/2012] [Accepted: 05/12/2012] [Indexed: 11/10/2022]
Abstract
Modeling conformational changes in protein docking calculations is challenging. To make the calculations tractable, most current docking algorithms typically treat proteins as rigid bodies and use soft scoring functions that implicitly accommodate some degree of flexibility. Alternatively, ensembles of structures generated from molecular dynamics (MD) may be cross-docked. However, such combinatorial approaches can produce many thousands or even millions of docking poses, and require fast and sensitive scoring functions to distinguish them. Here, we present a novel approach called "EigenHex," which is based on normal mode analyses (NMAs) of a simple elastic network model of protein flexibility. We initially assume that the proteins to be docked are rigid, and we begin by performing conventional soft docking using the Hex polar Fourier correlation algorithm. We then apply a pose-dependent NMA to each of the top 1000 rigid body docking solutions, and we sample and re-score multiple perturbed docking conformations generated from linear combinations of up to 20 eigenvectors using a multi-threaded particle swarm optimization algorithm. When applied to the 63 "rigid body" targets of the Protein Docking Benchmark version 2.0, our results show that sampling and re-scoring from just one to three eigenvectors gives a modest but consistent improvement for these targets. Thus, pose-dependent NMA avoids the need to sample multiple eigenvectors and it offers a promising alternative to combinatorial cross-docking.
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54
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Martin DR, Ozkan SB, Matyushov DV. Dissipative electro-elastic network model of protein electrostatics. Phys Biol 2012; 9:036004. [PMID: 22555305 DOI: 10.1088/1478-3975/9/3/036004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We propose a dissipative electro-elastic network model to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped dynamics of the normal modes of the network characterized by two friction coefficients. The electrostatic component is introduced to the model through atomic charges of the protein force field. The overall effect of the electrostatic fluctuations of the network is recorded through the frequency-dependent response functions of the electrostatic potential and electric field at the protein active site. We also consider the dynamics of displacements of individual residues in the network and the dynamics of distances between pairs of residues. The model is tested against loss spectra of residue displacements and the electrostatic potential and electric field at the heme's iron from all-atom molecular dynamics simulations of three hydrated globular proteins.
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Affiliation(s)
- Daniel R Martin
- Center for Biological Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
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55
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Atilgan C, Okan OB, Atilgan AR. Network-based models as tools hinting at nonevident protein functionality. Annu Rev Biophys 2012; 41:205-25. [PMID: 22404685 DOI: 10.1146/annurev-biophys-050511-102305] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Network-based models of proteins are popular tools employed to determine dynamic features related to the folded structure. They encompass all topological and geometric computational approaches idealizing proteins as directly interacting nodes. Topology makes use of neighborhood information of residues, and geometry includes relative placement of neighbors. Coarse-grained approaches efficiently predict alternative conformations because of inherent collectivity in the protein structure. Such collectivity is moderated by topological characteristics that also tune neighborhood structure: That rich residues have richer neighbors secures robustness toward random loss of interactions/nodes due to environmental fluctuations/mutations. Geometry conveys the additional information of force balance to network models, establishing the local shape of the energy landscape. Here, residue and/or bond perturbations are critically evaluated to suggest new experiments, as network-based computational techniques prove useful in capturing domain movements and conformational shifts resulting from environmental alterations. Evolutionarily conserved residues are optimally connected, defining a subnetwork that may be utilized for further coarsening.
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Affiliation(s)
- Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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56
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Dietzen M, Zotenko E, Hildebrandt A, Lengauer T. On the applicability of elastic network normal modes in small-molecule docking. J Chem Inf Model 2012; 52:844-56. [PMID: 22320151 DOI: 10.1021/ci2004847] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Incorporating backbone flexibility into protein-ligand docking is still a challenging problem. In protein-protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein-ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a set of conformations that optimally reproduce its C(α) trace with respect to the underlying normal mode subspace. Using AutoDock, GOLD, and FlexX we then docked the original ligands into these conformations to assess how the docking performance depends on the number of modes used to reproduce the holo structure. The results of our study indicate that, even for such a best-case scenario, the use of normal mode analysis in small-molecule docking is restricted and that a general rule on how many modes to use does not seem to exist or at least is not easy to find.
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57
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Abstract
Explicitly accounting for target flexibility in docking still constitutes a difficult challenge due to the high dimensionality of the conformational space to be sampled. This especially applies to the high-throughput scenario, where the screening of hundreds of thousands compounds takes place. The use of multiple receptor conformations (MRCs) to perform ensemble docking in a sequential fashion is a simple but powerful approach that allows to incorporate binding site structural diversity in the docking process. Whenever enough experimental structures to build a diverse ensemble are not available, normal mode analysis provides an appealing and efficient approach to in silico generate MRCs by distortion along few low-frequency modes that represent collective mid- and large-scale displacements. In this way, the dimension of the conformational space to be sampled is heavily reduced. This methodology is especially suited to incorporate target flexibility at the backbone level. In this chapter, the main components of normal mode-based approaches in the context of ensemble docking are presented and explained, including the theoretical and practical considerations needed for the successful development and implementation of this methodology.
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Affiliation(s)
- Claudio N Cavasotto
- School of Biomedical Informatics, The University of Texas Health Center, Houston, TX, USA.
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58
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Zheng W, Tekpinar M. Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell. Biophys J 2011; 101:2981-91. [PMID: 22208197 DOI: 10.1016/j.bpj.2011.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/06/2011] [Accepted: 11/04/2011] [Indexed: 01/16/2023] Open
Abstract
Small-angle x-ray scattering (SAXS) is a powerful technique widely used to explore conformational states and transitions of biomolecular assemblies in solution. For accurate model reconstruction from SAXS data, one promising approach is to flexibly fit a known high-resolution protein structure to low-resolution SAXS data by computer simulations. This is a highly challenging task due to low information content in SAXS data. To meet this challenge, we have developed what we believe to be a novel method based on a coarse-grained (one-bead-per-residue) protein representation and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method optimizes a pseudoenergy that combines the modified elastic-network model energy with a SAXS-fitting score and a collision energy that penalizes steric collisions. Our method uses what we consider a new implicit hydration shell model that accounts for the contribution of hydration shell to SAXS data accurately without explicitly adding waters to the system. We have rigorously validated our method using five test cases with simulated SAXS data and three test cases with experimental SAXS data. Our method has successfully generated high-quality structural models with root mean-squared deviation of 1 ∼ 3 Å from the target structures.
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Affiliation(s)
- Wenjun Zheng
- Physics Department, University at Buffalo, State University of New York, Buffalo, New York, USA.
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59
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Flores SC, Gerstein MB. Predicting protein ligand binding motions with the conformation explorer. BMC Bioinformatics 2011; 12:417. [PMID: 22032721 PMCID: PMC3354956 DOI: 10.1186/1471-2105-12-417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 10/27/2011] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Knowledge of the structure of proteins bound to known or potential ligands is crucial for biological understanding and drug design. Often the 3D structure of the protein is available in some conformation, but binding the ligand of interest may involve a large scale conformational change which is difficult to predict with existing methods. RESULTS We describe how to generate ligand binding conformations of proteins that move by hinge bending, the largest class of motions. First, we predict the location of the hinge between domains. Second, we apply an Euler rotation to one of the domains about the hinge point. Third, we compute a short-time dynamical trajectory using Molecular Dynamics to equilibrate the protein and ligand and correct unnatural atomic positions. Fourth, we score the generated structures using a novel fitness function which favors closed or holo structures. By iterating the second through fourth steps we systematically minimize the fitness function, thus predicting the conformational change required for small ligand binding for five well studied proteins. CONCLUSIONS We demonstrate that the method in most cases successfully predicts the holo conformation given only an apo structure.
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Affiliation(s)
- Samuel C Flores
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala, 75124, Sweden
| | - Mark B Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114 MBB, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, PO Box 208114 MBB, New Haven, CT, 06520, USA
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60
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Atilgan AR, Aykut AO, Atilgan C. Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. J Chem Phys 2011; 135:155102. [DOI: 10.1063/1.3651807] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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61
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Tran HT, Zhang S. Accurate prediction of the bound form of the Akt pleckstrin homology domain using normal mode analysis to explore structural flexibility. J Chem Inf Model 2011; 51:2352-60. [PMID: 21834588 DOI: 10.1021/ci2001742] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular docking is often performed with rigid receptors. This can be a serious limitation, since the receptor often differs between bound and unbound forms or between bound forms with different ligands. We recently developed a normal-mode based docking method and showed that it is possible to obtain reasonable estimates of the complexed form of the pleckstrin homology (PH) domain of Akt, starting with the free form of the receptor. With inositol (1,3,4,5)-tetrakisphosphate (IP4) as the ligand the docked results agree with the known high-resolution X-ray crystal structure of the IP4-Akt PH domain complex. We also tested our methods with PH4, SC66, and PIT-1, several recently designed PH domain inhibitors. The results are shown to be consistent with available experimental data and previous modeling studies. The method we described can be used for molecular docking analysis even when only an approximation of the experimental structure or model is known.
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Affiliation(s)
- Hoang T Tran
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas 77030, United States
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62
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Palmer DS, Jensen F. Predicting large-scale conformational changes in proteins using energy-weighted normal modes. Proteins 2011; 79:2778-93. [DOI: 10.1002/prot.23105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 05/04/2011] [Accepted: 05/19/2011] [Indexed: 11/10/2022]
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63
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Fernández JD, Vico FJ. Automating the search of molecular motor templates by evolutionary methods. Biosystems 2011; 106:82-93. [PMID: 21784125 DOI: 10.1016/j.biosystems.2011.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/30/2011] [Accepted: 07/06/2011] [Indexed: 01/10/2023]
Abstract
Biological molecular motors are nanoscale devices capable of transforming chemical energy into mechanical work, which are being researched in many scientific disciplines. From a computational point of view, the characteristics and dynamics of these motors are studied at multiple time scales, ranging from very detailed and complex molecular dynamics simulations spanning a few microseconds, to extremely simple and coarse-grained theoretical models of their working cycles. However, this research is performed only in the (relatively few) instances known from molecular biology. In this work, results from elastic network analysis and behaviour-finding methods are applied to explore a subset of the configuration space of template molecular structures that are able to transform chemical energy into directed movement, for a fixed instance of working cycle. While using methods based on elastic networks limits the scope of our results, it enables the implementation of computationally lightweight methods, in a way that evolutionary search techniques can be applied to discover novel molecular motor templates. The results show that molecular motion can be attained from a variety of structural configurations, when a functional working cycle is provided. Additionally, these methods enable a new computational way to test hypotheses about molecular motors.
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Affiliation(s)
- Jose D Fernández
- Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga, Severo Ochoa 4, 29590 Málaga, Spain.
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64
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Ahmed A, Rippmann F, Barnickel G, Gohlke H. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J Chem Inf Model 2011; 51:1604-22. [PMID: 21639141 DOI: 10.1021/ci100461k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 Å) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.
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Affiliation(s)
- Aqeel Ahmed
- Department of Biological Sciences, Molecular Bioinformatics Group, Goethe University, Frankfurt, Germany
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65
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Lill MA. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. Biochemistry 2011; 50:6157-69. [PMID: 21678954 DOI: 10.1021/bi2004558] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Flexibility and dynamics are protein characteristics that are essential for the process of molecular recognition. Conformational changes in the protein that are coupled to ligand binding are described by the biophysical models of induced fit and conformational selection. Different concepts that incorporate protein flexibility into protein-ligand docking within the context of these two models are reviewed. Several computational studies that discuss the validity and possible limitations of such approaches will be presented. Finally, different approaches that incorporate protein dynamics, e.g., configurational entropy, and solvation effects into docking will be highlighted.
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Affiliation(s)
- Markus A Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.
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66
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Schuyler AD, Carlson HA, Feldman EL. Computational methods for identifying a layered allosteric regulatory mechanism for ALS-causing mutations of Cu-Zn superoxide dismutase 1. Proteins 2011; 79:417-27. [PMID: 21104697 DOI: 10.1002/prot.22892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The most prominent form of familial amyotrophic lateral sclerosis (fALS, Lou Gehrig's Disease) is caused by mutations of Cu-Zn superoxide dismutase 1 (SOD1). SOD1 maintains antioxidant activity under fALS causing mutations, suggesting that the mutations introduce a new, toxic, function. There are 100+ such known mutations that are chemically diverse and spatially distributed across the structure. The common phenotype leads us to propose an allosteric regulatory mechanism hypothesis: SOD1 mutants alter the correlated dynamics of the structure and differentially signal across an inherent allosteric network, thereby driving the disease mechanism at varying rates of efficiency. Two recently developed computational methods for identifying allosteric control sites are applied to the wild type crystal structure, 4 fALS mutant crystal structures, 20 computationally generated fALS mutants and 1 computationally generated non-fALS mutant. The ensemble of mutant structures is used to generate an ensemble of dynamics, from which two allosteric control networks are identified. One network is connected to the catalytic site and thus may be involved in the natural antioxidant function. The second allosteric control network has a locus bordering the dimer interface and thus may serve as a mechanism to modulate dimer stability. Though the toxic function of mutated SOD1 is unknown and likely due to several contributing factors, this study explains how diverse mutations give rise to a common function. This new paradigm for allostery controlled function has broad implications across allosteric systems and may lead to the identification of the key chemical activity of SOD1-linked ALS.
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Affiliation(s)
- Adam D Schuyler
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
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67
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Ahmed A, Villinger S, Gohlke H. Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses. Proteins 2011; 78:3341-52. [PMID: 20848551 DOI: 10.1002/prot.22841] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A large-scale comparison of essential dynamics (ED) modes from molecular dynamic simulations and normal modes from coarse-grained normal mode methods (CGNM) was performed on a dataset of 335 proteins. As CGNM methods, the elastic network model (ENM) and the rigid cluster normal mode analysis (RCNMA) were used. Low-frequency normal modes from ENM correlate very well with ED modes in terms of directions of motions and relative amplitudes of motions. Notably, a similar performance was found if normal modes from RCNMA were used, despite a higher level of coarse graining. On average, the space spanned by the first quarter of ENM modes describes 84% of the space spanned by the five ED modes. Furthermore, no prominent differences for ED and CGNM modes among different protein structure classes (CATH classification) were found. This demonstrates the general potential of CGNM approaches for describing intrinsic motions of proteins with little computational cost. For selected cases, CGNM modes were found to be more robust among proteins that have the same topology or are of the same homologous superfamily than ED modes. In view of recent evidence regarding evolutionary conservation of vibrational dynamics, this suggests that ED modes, in some cases, might not be representative of the underlying dynamics that are characteristic of a whole family, probably due to insufficient sampling of some of the family members by MD.
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Affiliation(s)
- Aqeel Ahmed
- Department of Biological Sciences, Molecular Bioinformatics Group, Goethe-University, Frankfurt, Germany
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68
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Atilgan C, Gerek ZN, Ozkan SB, Atilgan AR. Manipulation of conformational change in proteins by single-residue perturbations. Biophys J 2010; 99:933-43. [PMID: 20682272 DOI: 10.1016/j.bpj.2010.05.020] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 05/03/2010] [Accepted: 05/07/2010] [Indexed: 11/28/2022] Open
Abstract
Using the perturbation-response scanning (PRS) technique, we study a set of 25 proteins that display a variety of conformational motions upon ligand binding (e.g., shear, hinge, allosteric). In most cases, PRS determines single residues that may be manipulated to achieve the resulting conformational change. PRS reveals that for some proteins, binding-induced conformational change may be achieved through the perturbation of residues scattered throughout the protein, whereas in others, perturbation of specific residues confined to a highly specific region is necessary. Overlaps between the experimental and PRS-calculated atomic displacement vectors are usually more descriptive of the conformational change than those obtained from a modal analysis of elastic network models. Furthermore, the largest overlaps obtained by the latter approach do not always appear in the most collective modes; there are cases where more than one mode yields comparable overlap sizes. We show that success of the modal analysis depends on an absence of redundant paths in the protein. PRS thus demonstrates that several relevant modes can be induced simultaneously by perturbing a single select residue on the protein. We also illustrate the biological relevance of applying PRS to the GroEL, adenylate kinase, myosin, and kinesin structures in detail by showing that the residues whose perturbation leads to precise conformational changes usually correspond to those experimentally determined to be functionally important.
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Affiliation(s)
- C Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Instanbul, Turkey.
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69
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Atilgan C, Okan OB, Atilgan AR. How orientational order governs collectivity of folded proteins. Proteins 2010; 78:3363-75. [PMID: 20818660 DOI: 10.1002/prot.22843] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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70
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Dykeman EC, Sankey OF. Normal mode analysis and applications in biological physics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:423202. [PMID: 21403307 DOI: 10.1088/0953-8984/22/42/423202] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies. The use of normal modes in the study of these motions is often extremely fruitful since many of the functional motions of large proteins can be described using just a few normal modes which are intimately related to the overall structure of the protein. In this review, we present a broad overview of several popular methods used in the study of normal modes in biological physics including continuum elastic theory, the elastic network model, and a new all-atom method, recently developed, which is capable of computing a subset of the low frequency vibrational modes exactly. After a review of the various methods, we present several examples of applications of normal modes in the study of functional motions, with an emphasis on viral capsids.
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Affiliation(s)
- Eric C Dykeman
- Department of Physics, Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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71
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Moal IH, Bates PA. SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci 2010; 11:3623-48. [PMID: 21152290 PMCID: PMC2996808 DOI: 10.3390/ijms11103623] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 07/29/2010] [Accepted: 09/16/2010] [Indexed: 11/17/2022] Open
Abstract
Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.
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Affiliation(s)
- Iain H. Moal
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London, WC2A 3LY, UK
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London, WC2A 3LY, UK
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72
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Bahar I. On the functional significance of soft modes predicted by coarse-grained models for membrane proteins. ACTA ACUST UNITED AC 2010; 135:563-73. [PMID: 20513758 PMCID: PMC2888054 DOI: 10.1085/jgp.200910368] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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73
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Cheng S, Niv MY. Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation. J Chem Inf Model 2010; 50:1602-10. [DOI: 10.1021/ci100076j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shu Cheng
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University, Rehovot 76100, Israel
| | - Masha Y. Niv
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University, Rehovot 76100, Israel
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74
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Lezon TR, Bahar I. Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology. PLoS Comput Biol 2010; 6:e1000816. [PMID: 20585542 PMCID: PMC2887458 DOI: 10.1371/journal.pcbi.1000816] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 05/13/2010] [Indexed: 11/19/2022] Open
Abstract
Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics. As more protein structures are solved, we are able to perform a more critical assessment of the relationship between protein structure and dynamics, and to gain a deeper understanding of the major determinants of structural dynamics. Here we perform a systematic study on a set of proteins structurally determined by NMR spectroscopy. The dynamics are analyzed using elastic network models and a novel method based on entropy maximization to demonstrate that properties such as contact order and secondary structure do play a role in defining the experimentally observed covariance data. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as well as stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics.
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Affiliation(s)
| | - Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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75
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Mashiach E, Nussinov R, Wolfson HJ. FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res 2010; 38:W457-61. [PMID: 20460459 PMCID: PMC2896170 DOI: 10.1093/nar/gkq373] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Protein–protein docking algorithms aim to predict the structure of a complex given the atomic structures of the proteins that assemble it. The docking procedure usually consists of two main steps: docking candidate generation and their refinement. The refinement stage aims to improve the accuracy of the candidate solutions and to identify near-native solutions among them. During protein–protein interaction, both side chains and backbone change their conformation. Refinement methods should model these conformational changes in order to obtain a more accurate model of the complex. Handling protein backbone flexibility is a major challenge for docking methodologies, since backbone flexibility adds a huge number of degrees of freedom to the search space. FiberDock is the first docking refinement web server, which accounts for both backbone and side-chain flexibility. Given a set of up to 100 potential docking candidates, FiberDock models the backbone and side-chain movements that occur during the interaction, refines the structures and scores them according to an energy function. The FiberDock web server is free and available with no login requirement at http://bioinfo3d.cs.tau.ac.il/FiberDock/.
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Affiliation(s)
- Efrat Mashiach
- Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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76
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Mashiach E, Nussinov R, Wolfson HJ. FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins 2010; 78:1503-19. [PMID: 20077569 PMCID: PMC4290165 DOI: 10.1002/prot.22668] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Upon binding, proteins undergo conformational changes. These changes often prevent rigid-body docking methods from predicting the 3D structure of a complex from the unbound conformations of its proteins. Handling protein backbone flexibility is a major challenge for docking methodologies, as backbone flexibility adds a huge number of degrees of freedom to the search space, and therefore considerably increases the running time of docking algorithms. Normal mode analysis permits description of protein flexibility as a linear combination of discrete movements (modes). Low-frequency modes usually describe the large-scale conformational changes of the protein. Therefore, many docking methods model backbone flexibility by using only few modes, which have the lowest frequencies. However, studies show that due to molecular interactions, many proteins also undergo local and small-scale conformational changes, which are described by high-frequency normal modes. Here we present a new method, FiberDock, for docking refinement which models backbone flexibility by an unlimited number of normal modes. The method iteratively minimizes the structure of the flexible protein along the most relevant modes. The relevance of a mode is calculated according to the correlation between the chemical forces, applied on each atom, and the translation vector of each atom, according to the normal mode. The results show that the method successfully models backbone movements that occur during molecular interactions and considerably improves the accuracy and the ranking of rigid-docking models of protein-protein complexes. A web server for the FiberDock method is available at: http://bioinfo3d.cs.tau.ac.il/FiberDock.
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Affiliation(s)
- Efrat Mashiach
- Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI–Frederick, Frederick, Maryland 21702
- Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim J. Wolfson
- Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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77
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Dykeman EC, Sankey OF. Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021918. [PMID: 20365606 DOI: 10.1103/physreve.81.021918] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 01/07/2010] [Indexed: 05/29/2023]
Abstract
We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (approximately 10) low-frequency modes that are global and cooperative.
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Affiliation(s)
- Eric C Dykeman
- Department of Physics, Center for Biological Physics, Arizona State University, Tempe, Arizona 85287-1504, USA
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78
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Batista PR, Robert CH, Maréchal JD, Hamida-Rebaï MB, Pascutti PG, Bisch PM, Perahia D. Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease. Phys Chem Chem Phys 2010; 12:2850-9. [DOI: 10.1039/b919148h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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79
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Izaguirre JA, Sweet CR, Pande VS. Multiscale dynamics of macromolecules using normal mode Langevin. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2010:240-51. [PMID: 19908376 PMCID: PMC4308582 DOI: 10.1142/9789814295291_0026] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins and other macromolecules have coupled dynamics over multiple time scales (from femtosecond to millisecond and beyond) that make resolving molecular dynamics challenging. We present an approach based on periodically decomposing the dynamics of a macromolecule into slow and fast modes based on a scalable coarse-grained normal mode analysis. A Langevin equation is used to propagate the slowest degrees of freedom while minimizing the nearly instantaneous degrees of freedom. We present numerical results showing that time steps of up to 1000 fs can be used, with real speedups of up to 200 times over plain molecular dynamics. We present results of successfully folding the Fip35 mutant of WW domain.
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Affiliation(s)
| | - C. R. Sweet
- Center for Research Computing, Univ. of Notre Dame, Notre Dame, IN 46556 USA
| | - V. S. Pande
- Dept. of Chemistry, Stanford University, Stanford CA 94305 USA
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80
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Wells SA, Jimenez-Roldan JE, Römer RA. Comparative analysis of rigidity across protein families. Phys Biol 2009; 6:046005. [DOI: 10.1088/1478-3975/6/4/046005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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81
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Li DW, Brüschweiler R. All-atom contact model for understanding protein dynamics from crystallographic B-factors. Biophys J 2009; 96:3074-81. [PMID: 19383453 DOI: 10.1016/j.bpj.2009.01.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 12/29/2008] [Accepted: 01/12/2009] [Indexed: 01/03/2023] Open
Abstract
An all-atom local contact model is described that can be used to predict protein motions underlying isotropic crystallographic B-factors. It uses a mean-field approximation to represent the motion of an atom in a harmonic potential generated by the surrounding atoms resting at their equilibrium positions. Based on a 400-ns molecular dynamics simulation of ubiquitin in explicit water, it is found that each surrounding atom stiffens the spring constant by a term that on average scales exponentially with the interatomic distance. This model combines features of the local density model by Halle and the local contact model by Zhang and Brüschweiler. When applied to a nonredundant set of 98 ultra-high resolution protein structures, an average correlation coefficient of 0.75 is obtained for all atoms. The systematic inclusion of crystal contact contributions and fraying effects is found to enhance the performance substantially. Because the computational cost of the local contact model scales linearly with the number of protein atoms, it is applicable to proteins of any size for the prediction of B-factors of both backbone and side-chain atoms. The model performs as well as or better than several other models tested, such as rigid-body motional models, the local density model, and various forms of the elastic network model. It is concluded that at the currently achievable level of accuracy, collective intramolecular motions are not essential for the interpretation of B-factors.
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Affiliation(s)
- Da-Wei Li
- Chemical Sciences Laboratory, Department of Chemistry and Biochemistry, and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
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82
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Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol 2009; 5:e1000360. [PMID: 19381265 PMCID: PMC2664929 DOI: 10.1371/journal.pcbi.1000360] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 03/13/2009] [Indexed: 11/19/2022] Open
Abstract
Identification of pathways involved in the structural transitions of biomolecular
systems is often complicated by the transient nature of the conformations
visited across energy barriers and the multiplicity of paths accessible in the
multidimensional energy landscape. This task becomes even more challenging in
exploring molecular systems on the order of megadaltons. Coarse-grained models
that lend themselves to analytical solutions appear to be the only possible
means of approaching such cases. Motivated by the utility of elastic network
models for describing the collective dynamics of biomolecular systems and by the
growing theoretical and experimental evidence in support of the intrinsic
accessibility of functional substates, we introduce a new method,
adaptive anisotropic network model (aANM),
for exploring functional transitions. Application to bacterial chaperonin GroEL
and comparisons with experimental data, results from action minimization
algorithm, and previous simulations support the utility of aANM
as a computationally efficient, yet physically plausible, tool for unraveling
potential transition pathways sampled by large complexes/assemblies. An
important outcome is the assessment of the critical inter-residue interactions
formed/broken near the transition state(s), most of which involve conserved
residues. Most proteins are biomolecular machines. They perform their function by
undergoing changes between different structures. Understanding the mechanism of
transition between these structures is of major importance to design methods for
controlling such transitions, and thereby modulating protein function. Although
there are many computational methods for exploring the transitions of small
proteins, the task of exploring the transition pathways becomes prohibitively
expensive in the case of supramolecular systems. The bacterial chaperonin GroEL
is such a supramolecular machine. It plays an important role in assisting
protein folding. During its function, GroEL undergoes structural transitions
between multiple forms. Here, we are introducing a new methodology, based on
elastic network models, for elucidating the transition mechanisms in such
supramolecular systems. Application to GroEL provides us with biologically
significant information on critical interactions and sequence of events
occurring during the chaperonin machinery and key contacts that make and break
at the transition. The method can be readily applied to other supramolecular
machines.
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83
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Andrusier N, Mashiach E, Nussinov R, Wolfson HJ. Principles of flexible protein-protein docking. Proteins 2009; 73:271-89. [PMID: 18655061 DOI: 10.1002/prot.22170] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein-protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre-generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small-scale movements of the backbone and side-chains are modeled and the binding orientation is improved by rigid-body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem.
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Affiliation(s)
- Nelly Andrusier
- School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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84
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85
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Hills RD, Brooks CL. Insights from coarse-grained Gō models for protein folding and dynamics. Int J Mol Sci 2009; 10:889-905. [PMID: 19399227 PMCID: PMC2672008 DOI: 10.3390/ijms10030889] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 02/23/2009] [Accepted: 02/26/2009] [Indexed: 12/17/2022] Open
Abstract
Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions.
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Affiliation(s)
- Ronald D. Hills
- Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. TPC6 La Jolla, CA 92037, USA
| | - Charles L. Brooks
- Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. TPC6 La Jolla, CA 92037, USA
- Department of Chemistry and Biophysics Program, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109, USA
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +1-734-647-6682; Fax: +1-734-647-1604
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86
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Schuyler AD, Jernigan RL, Qasba PK, Ramakrishnan B, Chirikjian GS. Iterative cluster-NMA: A tool for generating conformational transitions in proteins. Proteins 2009; 74:760-76. [PMID: 18712827 DOI: 10.1002/prot.22200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Computational models provide insight into the structure-function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this article, the iterative cluster-NMA (icNMA) method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate structures to define the local accessible motion space, and thus produce an appropriate displacement. Following the derivation of the icNMA method, a set of sample simulations are performed to probe the robustness of the model. A detailed analysis of beta1,4-galactosyltransferase-T1 is also given, to highlight many of the capabilities of icNMA. Remarkably, during the transition, a helix is seen to be extended by an additional turn, emphasizing a new unknown role for secondary structures to absorb slack during transitions. The transition pathway for adenylate kinase, which has been frequently studied in the literature, is also discussed.
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Affiliation(s)
- Adam D Schuyler
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, USA
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87
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Allosteric communication in myosin V: from small conformational changes to large directed movements. PLoS Comput Biol 2008; 4:e1000129. [PMID: 18704171 PMCID: PMC2497441 DOI: 10.1371/journal.pcbi.1000129] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Accepted: 06/17/2008] [Indexed: 11/21/2022] Open
Abstract
The rigor to post-rigor transition in myosin, a consequence of ATP binding, plays an essential role in the Lymn–Taylor functional cycle because it results in the dissociation of the actomyosin complex after the powerstroke. On the basis of the X-ray structures of myosin V, we have developed a new normal mode superposition model for the transition path between the two states. Rigid-body motions of the various subdomains and specific residues at the subdomain interfaces are key elements in the transition. The allosteric communication between the nucleotide binding site and the U50/L50 cleft is shown to result from local changes due to ATP binding, which induce large amplitude motions that are encoded in the structure of the protein. The triggering event is the change in the interaction of switch I and the P-loop, which is stabilized by ATP binding. The motion of switch I, which is a relatively rigid element of the U50 subdomain, leads directly to a partial opening of the U50/L50 cleft; the latter is expected to weaken the binding of myosin to actin. The calculated transition path demonstrates the nature of the subdomain coupling and offers an explanation for the mutual exclusion of ATP and actin binding. The mechanism of the uncoupling of the converter from the motor head, an essential part of the transition, is elucidated. The origin of the partial untwisting of the central β-sheet in the rigor to post-rigor transition is described. Myosins are molecular motor proteins that interact with actin filaments to perform a wide range of cellular functions. They use the universal energy storage molecule adenosine triphosphate (ATP). The functional cycle involves myosin binding to actin, a “powerstroke” leading to directed movement, and myosin release in preparation for the next step. A fundamental question concerns the mechanism by which the local structural changes due to ATP binding, hydrolysis, and products release can generate the large myosin changes of conformation required for this cycle. Here, we focus on the rigor to post-rigor transition of myosin V, which results in the release of myosin from actin. Starting from the X-ray structures of the two states, we have used the optimal superposition of normal modes to determine the transition path. The path shows the allosteric mechanism by which ATP binding leads to the opening of the U50/L50 cleft, the essential step in the unbinding of myosin from actin. More generally, the new normal-mode superposition model can be useful for describing large-amplitude conformational transitions encoded in protein structures by evolution.
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88
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Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes. Biophys J 2008; 95:5862-73. [PMID: 18676657 DOI: 10.1529/biophysj.107.128447] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Conformational transitions between open/closed or free/bound states in proteins possess functional importance. We propose a technique in which the collective modes obtained from an anisotropic network model (ANM) are used in conjunction with a Monte Carlo (MC) simulation approach, to investigate conformational transition pathways and pathway intermediates. The ANM-MC technique is applied to adenylate kinase (AK) and hemoglobin. The iterative method, in which normal modes are continuously updated during the simulation, proves successful in accomplishing the transition between open-closed conformations of AK and tense-relaxed forms of hemoglobin (C(alpha)-root mean square deviations between two end structures of 7.13 A and 3.55 A, respectively). Target conformations are reached by root mean-square deviations of 2.27 A and 1.90 A for AK and hemoglobin, respectively. The intermediate conformations overlap with crystal structures from the AK family within a 3.0-A root mean-square deviation. In the case of hemoglobin, the transition of tense-to-relaxed passes through the relaxed state. In both cases, the lowest-frequency modes are effective during transitions. The targeted Monte Carlo approach is used without the application of collective modes. Both the ANM-MC and targeted Monte Carlo techniques can explore sequences of events in transition pathways with an efficient yet realistic conformational search.
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89
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Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophys J 2008; 95:4183-92. [PMID: 18658214 DOI: 10.1529/biophysj.108.139733] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a method to parameterize heterogeneous elastic network models (heteroENMs) of proteins to reproduce the fluctuations observed in atomistic simulations. Because it is based on atomistic simulation, our method allows the development of elastic coarse-grained models of proteins under different conditions or in different environments. The method is simple and applicable to models at any level of coarse-graining. We validated the method in three systems. First, we computed the persistence length of ADP-bound F-actin, using a heteroENM model. The value of 6.1 +/- 1.6 microm is consistent with the experimentally measured value of 9.0 +/- 0.5 microm. We then compared our method to a uniform elastic network model and a realistic extension algorithm via covariance Hessian (REACH) model of carboxy myoglobin, and found that the heteroENM method more accurately predicted mean-square fluctuations of alpha-carbon atoms. Finally, we showed that the method captures critical differences in effective harmonic interactions for coarse-grained models of the N-terminal Bin/amphiphysin/Rvs (N-BAR) domain of amphiphysin, by building models of N-BAR both bound to a membrane and free in solution.
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90
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Sweet CR, Petrone P, Pande VS, Izaguirre JA. Normal mode partitioning of Langevin dynamics for biomolecules. J Chem Phys 2008; 128:145101. [PMID: 18412479 DOI: 10.1063/1.2883966] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We propose a novel normal mode multiple time stepping Langevin dynamics integrator called NML. The aim is to approximate the kinetics or thermodynamics of a biomolecule by a reduced model based on a normal mode decomposition of the dynamical space. Our basis set uses the eigenvectors of a mass reweighted Hessian matrix calculated with a biomolecular force field. This particular choice has the advantage of an ordering according to the eigenvalues, which have a physical meaning of being the square of the mode frequency. Low frequency eigenvalues correspond to more collective motions, whereas the highest frequency eigenvalues are the limiting factor for the stability of the integrator. In NML, the higher frequency modes are overdamped and relaxed near their energy minimum while respecting the subspace of low frequency dynamical modes. Our numerical results confirm that both sampling and rates are conserved for an implicitly solvated alanine dipeptide model, with only 30% of the modes propagated, when compared to the full model. For implicitly solvated systems, NML gives a twofold improvement in efficiency over plain Langevin dynamics for sampling a small 22 atom (alanine dipeptide) model and in excess of an order of magnitude for sampling an 882 atom (bovine pancreatic trypsin inhibitor) model, with good scaling with system size subject to the number of modes propagated. NML has been implemented in the open source software PROTOMOL.
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Affiliation(s)
- Christopher R Sweet
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana, 46556, USA
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91
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Niv MY, Filizola M. Influence of oligomerization on the dynamics of G-protein coupled receptors as assessed by normal mode analysis. Proteins 2008; 71:575-86. [PMID: 17963239 DOI: 10.1002/prot.21787] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The recently discovered impact of oligomerization on G-protein coupled receptor (GPCR) function further complicates the already challenging goal of unraveling the molecular and dynamic mechanisms of these receptors. To help understand the effect of oligomerization on the dynamics of GPCRs, we have compared the motion of monomeric, dimeric, and tetrameric arrangements of the prototypic GPCR rhodopsin, using an approximate-yet powerful-normal mode analysis (NMA) technique termed elastic network model (ENM). Moreover, we have used ENM to discriminate between putative dynamic mechanisms likely to account for the recently observed conformational rearrangement of the TM4,5-TM4,5 dimerization interface of GPCRs that occurs upon activation. Our results indicate: (1) significant perturbation of the normal modes (NMs) of the rhodopsin monomer upon oligomerization, which is mainly manifested at interfacial regions; (2) increased positive correlation among the transmembrane domains (TMs) and between the extracellular loop (EL) and TM regions of the rhodopsin protomer; (3) highest interresidue positive correlation at the interfaces between protomers; and (4) experimentally testable hypotheses of differential motional changes within different putative oligomeric arrangements.
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Affiliation(s)
- Masha Y Niv
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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92
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Nucci NV, Scott JN, Vanderkooi JM. Coupling of complex aromatic ring vibrations to solvent through hydrogen bonds: effect of varied on-ring and off-ring hydrogen-bonding substitutions. J Phys Chem B 2008; 112:4022-35. [PMID: 18331017 DOI: 10.1021/jp0758770] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we examine the coupling of a complex ring vibration to solvent through hydrogen-bonding interactions. We compare phenylalanine, tyrosine, l-dopa, dopamine, norepinephrine, epinephrine, and hydroxyl-dl-dopa, a group of physiologically important small molecules that vary by single differences in H-bonding substitution. By examination of the temperature dependence of infrared absorptions of these molecules, we show that complex, many-atom vibrations can be coupled to solvent through hydrogen bonds and that the extent of that coupling is dependent on the degree of both on- and off-ring H-bonding substitution. The coupling is seen as a temperature-dependent frequency shift in infrared spectra, but the determination of the physical origin of that shift is based on additional data from temperature-dependent optical experiments and ab initio calculations. The optical experiments show that these small molecules are most sensitive to their immediate H-bonding environment rather than to bulk solvent properties. Ab initio calculations demonstrate H-bond-mediated vibrational coupling for the system of interest and also show that the overall small molecule solvent dependence is determined by a complex interplay of specific interactions and bulk solvation characteristics. Our findings indicate that a full understanding of biomolecule vibrational properties must include consideration of explicit hydrogen-bonding interactions with the surrounding microenvironment.
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Affiliation(s)
- Nathaniel V Nucci
- Department of Biochemistry and Biophysics, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA.
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93
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Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure 2008; 16:295-307. [PMID: 18275820 PMCID: PMC2409374 DOI: 10.1016/j.str.2007.11.016] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 11/20/2007] [Accepted: 11/26/2007] [Indexed: 11/23/2022]
Abstract
For many macromolecular assemblies, both a cryo-electron microscopy map and atomic structures of its component proteins are available. Here we describe a method for fitting and refining a component structure within its map at intermediate resolution (<15 A). The atomic positions are optimized with respect to a scoring function that includes the crosscorrelation coefficient between the structure and the map as well as stereochemical and nonbonded interaction terms. A heuristic optimization that relies on a Monte Carlo search, a conjugate-gradients minimization, and simulated annealing molecular dynamics is applied to a series of subdivisions of the structure into progressively smaller rigid bodies. The method was tested on 15 proteins of known structure with 13 simulated maps and 3 experimentally determined maps. At approximately 10 A resolution, Calpha rmsd between the initial and final structures was reduced on average by approximately 53%. The method is automated and can refine both experimental and predicted atomic structures.
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Affiliation(s)
- Maya Topf
- School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom.
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94
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Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models. Biophys J 2008; 94:3424-35. [PMID: 18223005 DOI: 10.1529/biophysj.107.120733] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With recent advances in single-molecule manipulation techniques, it is now possible to measure the mechanical resistance of proteins to external pulling forces applied at specific positions. Remarkably, such recent studies demonstrated that the pulling/stretching forces required to initiate unfolding vary considerably depending on the location of the application of the forces, unraveling residue/position-specific response of proteins to uniaxial tension. Here we show that coarse-grained elastic network models based on the topology of interresidue contacts in the native state can satisfactory explain the relative sizes of such stretching forces exerted on different residue pairs. Despite their simplicity, such models presumably capture a fundamental property that dominates the observed behavior: deformations that can be accommodated by the relatively lower frequency modes of motions intrinsically favored by the structure require weaker forces and vice versa. The mechanical response of proteins to external stress is therefore shown to correlate with the anisotropic fluctuation dynamics intrinsically accessible in the folded state. The dependence on the overall fold implies that evolutionarily related proteins sharing common structural features tend to possess similar mechanical properties. However, the theory cannot explain the differences observed in a number of structurally similar but sequentially distant domains, such as the fibronectin domains.
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95
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Abstract
Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our method but also point out the importance of incorporating surface structural water in studying protein dynamics.
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96
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Laine E, Yoneda JD, Blondel A, Malliavin TE. The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis. Proteins 2008; 71:1813-29. [DOI: 10.1002/prot.21862] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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97
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May A, Zacharias M. Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking. Proteins 2008; 70:794-809. [PMID: 17729269 DOI: 10.1002/prot.21579] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein-protein association can frequently involve significant backbone conformational changes of the protein partners. A computationally rapid method has been developed that allows to approximately account for global conformational changes during systematic protein-protein docking starting from many thousands of start configurations. The approach employs precalculated collective degrees of freedom as additional variables during protein-protein docking minimization. The global collective degrees of freedom are obtained from normal mode analysis using a Gaussian network model for the protein. Systematic docking searches were performed on 10 test systems that differed in the degree of conformational change associated with complex formation and in the degree of overlap between observed conformational changes and precalculated flexible degrees of freedom. The results indicate that in case of docking searches that minimize the influence of local side chain conformational changes inclusion of global flexibility can significantly improve the agreement of the near-native docking solutions with the corresponding experimental structures. For docking of unbound protein partners in several cases an improved ranking of near native docking solutions was observed. This was achieved at a very modest ( approximately 2-fold) increase of computational demands compared to rigid docking. For several test cases the number of docking solutions close to experiment was also significantly enhanced upon inclusion of soft collective degrees of freedom. This result indicates that inclusion of global flexibility can facilitate in silico protein-protein association such that a greater number of different start configurations results in favorable complex formation.
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Affiliation(s)
- Andreas May
- School of Engineering and Science, Jacobs University Bremen, D-28759 Bremen, Germany
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98
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Leherte L, Vercauteren DP. Collective motions of rigid fragments in protein structures from smoothed electron density distributions. J Comput Chem 2008; 29:1472-89. [DOI: 10.1002/jcc.20908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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99
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Delarue M. Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2007; 64:40-8. [PMID: 18094466 PMCID: PMC2394787 DOI: 10.1107/s0907444907053516] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 10/26/2007] [Indexed: 01/08/2023]
Abstract
Normal-mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular-replacement solution. Here, it is shown that it is also possible to directly refine the amplitudes of the normal modes against experimental data (X-ray or cryo-EM), generalizing rigid-body refinement methods by adding just a few additional degrees of freedom that sample collective and large-amplitude movements. It is also argued that the situation where several (conformations of) models are present simultaneously in the crystal can be studied with adjustable occupancies using techniques derived from statistical thermodynamics and already used in molecular modelling.
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Affiliation(s)
- Marc Delarue
- Unité de Dynamique Structurale des Macromolecules, Departement de Biologie Structurale et Chimie, URA 2185 du CNRS, Institut Pasteur, 25 Rue du Dr Roux, 75015 Paris, France.
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100
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Quapp W. Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine. J Comput Chem 2007; 28:1834-47. [PMID: 17342714 DOI: 10.1002/jcc.20688] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report a new, high-dimensional application of a method for finding a transition state (TS) between a reactant and a product on the potential energy surface: the search of a growing string along a reaction path defined by any Newton trajectory in combination with the Berny method (Quapp, J Chem Phys (2005), 122, 174106; we have provided this algorithm on a web page). Two given minima are connected by a one-dimensional, but usually curvilinear reaction coordinate. It leads to the TS region. The application of the method to alanine dipeptide finds the TS of the isomerisation C(7 ax) --> C(5), some TSs of the enantiomerisation of C(7 ax) from L-form to quasi-D-form, and it finds the TS region of a transition of a partly unfolded, bent structure which turns back into a mainly alpha-helix in the Ac(Ala)(15)NHMe polyalanine (all at the quantum mechanical level B3LYP/6-31G: the growing string calculation is interfaced with the Gaussian03 package). The formation or dissolvation of some alpha- or 3(10)-hydrogen bonds of the helix are discussed along the TS pathway, as well as the case of an enantiomer at the central residue of the helix.
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Affiliation(s)
- Wolfgang Quapp
- Mathematical Institute, University of Leipzig, Augustus-Platz, D-04109 Leipzig, Germany.
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