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Yatawara AK, Hodoscek M, Mierke DF. Ligand binding site identification by higher dimension molecular dynamics. J Chem Inf Model 2013; 53:674-80. [PMID: 23394112 DOI: 10.1021/ci300561b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We propose a new molecular dynamics (MD) protocol to identify the binding site of a guest within a host. The method utilizes a four spatial (4D) dimension representation of the ligand allowing for rapid and efficient sampling within the receptor. We applied the method to two different model receptors characterized by diverse structural features of the binding site and different ligand binding affinities. The Abl kinase domain is comprised of a deep binding pocket and displays high affinity for the two chosen ligands examined here. The PDZ1 domain of PSD-95 has a shallow binding pocket that accommodates a peptide ligand involving far fewer interactions and a micromolar affinity. To ensure completely unbiased searching, the ligands were placed in the direct center of the protein receptors, away from the binding site, at the start of the 4D MD protocol. In both cases, the ligands were successfully docked into the binding site as identified in the published structures. The 4D MD protocol is able to overcome local energy barriers in locating the lowest energy binding pocket and will aid in the discovery of guest binding pockets in the absence of a priori knowledge of the site of interaction.
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Affiliation(s)
- Achani K Yatawara
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
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2
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Toon A, Williams G. A dynamical approach to contact distance based protein structure determination. J Mol Graph Model 2011; 32:75-81. [PMID: 22088762 DOI: 10.1016/j.jmgm.2011.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/07/2011] [Accepted: 10/12/2011] [Indexed: 10/15/2022]
Abstract
Protein native structure topology based folding dynamics captures many aspects of protein folding. The fact that folding is driven by a potential derived only from residue pairs in native contact, a sparse distance matrix, lead us to postulate this as a solution method to the molecular distance geometry problem. In the standard Go model non-bonded residues move under the influence of a Lennard-Jones potential and consequently folding is slow. In this study we apply a faster quadratic potential Go model to solving the full-atom distance geometry problem, where distance data is based only on residue atoms within 5 Å in the native structure. We show that the method works well when only atomic contact data is known and when a substantial proportion of this contact data is missing. Also, we show that the method can be applied in conjunction with secondary structure prediction schemes to enhance accuracy in cases of missing contact data.
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Affiliation(s)
- Andrew Toon
- SIM University, School of Science and Technology, Singapore, Singapore
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3
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van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, Yu HB. Biomolecular modeling: Goals, problems, perspectives. Angew Chem Int Ed Engl 2007; 45:4064-92. [PMID: 16761306 DOI: 10.1002/anie.200502655] [Citation(s) in RCA: 444] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.
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Affiliation(s)
- Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland.
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4
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Torda AE, Van Gunsteren WF. Molecular Modeling Using Nuclear Magnetic Resonance Data. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125809.ch3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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5
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Leach AR. A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125793.ch1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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6
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van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, Yu HB. Biomolekulare Modellierung: Ziele, Probleme, Perspektiven. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502655] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Jansen TLC, Zhuang W, Mukamel S. Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanine. J Chem Phys 2004; 121:10577-98. [PMID: 15549941 DOI: 10.1063/1.1807824] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The line shapes detected in coherent femtosecond vibrational spectroscopies contain direct signatures of peptide conformational fluctuations through their effect on vibrational frequencies and intermode couplings. These effects are simulated in trialanine using a Green's function solution of a stochastic Liouville equation constructed for four collective bath coordinates (two Ramachandran angles affecting the mode couplings and two diagonal energies). We find that fluctuations of the Ramachandran angles which hardly affect the linear absorption can be effectively probed by two-dimensional spectra. The signal generated at k(1)+k(2)-k(3) is particularly sensitive to such fluctuations.
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Tappura K. Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations. Proteins 2001; 44:167-79. [PMID: 11455590 DOI: 10.1002/prot.1082] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An adjustable-barrier dihedral angle potential was added as an extension to a novel, previously presented soft-core potential to study its contribution to the efficacy of the search of the conformational space in molecular dynamics. As opposed to the conventional soft-core potential functions, the leading principle in the design of the new soft-core potential, as well as of its extension, the soft-core and adjustable-barrier dihedral angle (SCADA) potential (referred as the SCADA potential), was to maintain the main equilibrium properties of the original force field. This qualifies the methods for a variety of a priori modeling problems without need for additional restraints typically required with the conventional soft-core potentials. In the present study, the different potential energy functions are applied to the problem of predicting loop conformations in proteins. Comparison of the performance of the soft-core and SCADA potential showed that the main hurdles for the efficient sampling of the conformational space of (loops in) proteins are related to the high-energy barriers caused by the Lennard-Jones and Coulombic energy terms, and not to the rotational barriers, although the conformational search can be further enhanced by lowering the rotational barriers of the dihedral angles. Finally, different evaluation methods were studied and a few promising criteria found to distinguish the near-native loop conformations from the wrong ones.
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9
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Tappura K, Lahtela-Kakkonen M, Teleman O. A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations. J Comput Chem 2000. [DOI: 10.1002/(sici)1096-987x(20000415)21:5<388::aid-jcc5>3.0.co;2-m] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Huber T, Torda AE, van Gunsteren WF. Optimization methods for conformational sampling using a Boltzmann-weighted mean field approach. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199607)39:1<103::aid-bip11>3.0.co;2-h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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11
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Grdadolnik SG, Mierke DF. Structural characterization of the molecular dimer of the peptide antibiotic vancomycin by distance geometry in four spatial dimensions. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 1997; 37:1044-7. [PMID: 9392857 DOI: 10.1021/ci970233i] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The conformation of a dimer of the peptide antibiotic vancomycin is developed from computer simulations based on experimental distance constraints derived from high-resolution NMR measurements. The conformation and topological array of the dimer are determined by a distance geometry based method using the molecules cast into four spatial dimensions. This method was imperative for the refinement of vancomycin given the entwining of the monomers (including hydrogen bonding and interactions between the aromatic ring systems) within the dimer. The development of the high-resolution structure of the monomer and then simple molecular modeling to create the dimer which fulfills all of the experimental observations was not possible. In contrast, the refinement protocol using the dimer cast into four spatial dimensions was able to quickly locate conformations in which both the intra- and intermolecular nuclear Overhauser effects were satisfied. These structures, once converted back to three dimensions, were further refined using standard molecular mechanics energy minimization. The structural characteristics of the dimer with respect to binding to the cell-wall precursor are described.
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Chapman D. The measurement of molecular diversity: a three-dimensional approach. J Comput Aided Mol Des 1996; 10:501-12. [PMID: 9007684 DOI: 10.1007/bf00134174] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This paper describes a method for selecting a small, highly diverse subset from a large pool of molecules. The method has been employed in the design of combinatorial synthetic libraries for use in high-throughput screening for pharmaceutical lead generation. It computes diversity in terms of the main factors relevant to ligand-protein binding, namely the three-dimensional arrangement of steric bulk and of polar functionalities and molecular entropy. The method was used to select a set of 20 carboxylates suitable for use as side-chain precursors in a polyamine-based library. The method depends on estimates of various physical-chemical parameters involved in ligand-protein binding; experiments examined the sensitivity of the method to these parameters. This paper compares the diversity of randomly and rationally selected side-chain sets; the results suggest that careful design of synthetic combinatorial libraries may increase their effectiveness several-fold.
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Affiliation(s)
- D Chapman
- Afferent Systems Inc., San Francisco, CA 94114, USA
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Abstract
In the past years, much effort has been put on the development of new methodologies and algorithms for the prediction of protein secondary and tertiary structures from (sequence) data; this is reviewed in detail. New approaches for these predictions such as neural network methods, genetic algorithms, machine learning, and graph theoretical methods are discussed. Secondary structure prediction algorithms were improved mostly by considering families of related proteins; however, for the reliable tertiary structure modeling of proteins, knowledge-based techniques are still preferred. Methods and examples with more or less successful results are described. Also, programs and parameterizations for energy minimisations, molecular dynamics, and electrostatic interactions have been improved, especially with respect to their former limits of applicability. Other topics discussed in this review include the use of traditional and on-line databases, the docking problem and surface properties of biomolecules, packing of protein cores, de novo design and protein engineering, prediction of membrane protein structures, the verification and reliability of model structures, and progress made with currently available software and computer hardware. In summary, the prediction of the structure, function, and other properties of a protein is still possible only within limits, but these limits continue to be moved.
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Affiliation(s)
- G Böhm
- Institut für Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Germany
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Huber T, Torda AE, van Gunsteren WF. Local elevation: a method for improving the searching properties of molecular dynamics simulation. J Comput Aided Mol Des 1994; 8:695-708. [PMID: 7738605 DOI: 10.1007/bf00124016] [Citation(s) in RCA: 397] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.
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Affiliation(s)
- T Huber
- Physical Chemistry, ETH Zentrum, CH-8092 Zürich, Switzerland
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15
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Maranas CD, Floudas CA. A deterministic global optimization approach for molecular structure determination. J Chem Phys 1994. [DOI: 10.1063/1.467236] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Snow ME. A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules. Proteins 1993; 15:183-90. [PMID: 8441753 DOI: 10.1002/prot.340150208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A novel scheme for the parameterization of a type of "potential energy" function for protein molecules is introduced. The function is parameterized based on the known conformations of previously determined protein structures and their sequence similarity to a molecule whose conformation is to be calculated. Once parameterized, minima of the potential energy function can be located using a version of simulated annealing which has been previously shown to locate global and near-global minima with the given functional form. As a test problem, the potential was parameterized based on the known structures of the rubredoxins from Desulfovibrio vulgaris, Desulfovibrio desulfuricans, and Clostridium pasteurianum, which vary from 45 to 54 amino acids in length, and the sequence alignments of these molecules with the rubredoxin sequence from Desulfovibrio gigas. Since the Desulfovibrio gigas rubredeoxin conformation has also been determined, it is possible to check the accuracy of the results. Ten simulated-annealing runs from random starting conformations were performed. Seven of the 10 resultant conformations have an all-C alpha rms deviation from the crystallographically determined conformation of less than 1.7 A. For five of the structures, the rms deviation is less than 0.8 A. Four of the structures have conformations which are virtually identical to each other except for the position of the carboxy-terminal residue. This is also the conformation which is achieved if the determined crystal structure is minimized with the same potential. The all-C alpha rms difference between the crystal and minimized crystal structures is 0.6 A.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M E Snow
- University of Michigan Information Technology Division, Ann Arbor 48103-4943
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17
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Snow ME. Powerful simulated-annealing algorithm locates global minimum of protein-folding potentials from multiple starting conformations. J Comput Chem 1992. [DOI: 10.1002/jcc.540130507] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Abstract
A fundamental problem in molecular biology is the determination of the conformation of macromolecules from NMR data. Several successful distance geometry programs have been developed for this purpose, for example DISGEO. A particularly difficult facet of these programs is the embedding problem, that is the problem of determining those conformations whose distances between atoms are nearest those measured by the NMR techniques. The embedding problem is the distance geometry equivalent of the multiple minima problem, which arises in energy minimization approaches to conformation determination. We show that the distance geometry approach has some nice geometry not associated with other methods that allows one to prove detailed results with regard to the location of local minima. We exploit this geometry to develop some algorithms which are faster and find more minima than the algorithms presently used.
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Affiliation(s)
- W Glunt
- Department of Mathematics, University of Kentucky, Lexington 40506
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