Molecular dynamics simulations of Leu-enkephalin in water and DMSO

Spoel, David van der; Berendsen, H.J.C.

doi:10.1016/s0006-3495(97)78847-7

Cited by 116 publications

(106 citation statements)

References 52 publications

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“…The protein was embedded in a box containing SPC model water [41] that extended to at least 8Å between the protein and the edge of the box. Although more complex water models are nowadays frequently used in the simulation of proteins, we chose to use the SPC, as it was found to give superior results for simulations of solutes in water when compared to more sophisticated water models [42], especially at interfaces [43]. The total number of water molecules was 6677.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Protein Surface Dynamics: Interaction with Water and Small Solutes

2005

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Abstract. Previous time resolved measurements had indicated that protons could propagate on the surface of a protein, or a membrane, by a special mechanism that enhances the shuttle of the proton towards a specific site [1]. It was proposed that a proper location of residues on the surface contributes to the proton shuttling function. In the present study, this notion was further investigated using molecular dynamics, with only the mobile charge replaced by Na + and Cl − ions. A molecular dynamics simulation of a small globular protein (the S6 of the bacterial ribosome) was carried out in the presence of explicit water molecules and four pairs of Na + and Cl − ions. A 10 ns simulation indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. Yet it was noted that, close to some domains, the ions extended their duration near the surface, suggesting that the local electrostatic potential prevented them from diffusing to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.

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Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Protein Surface Dynamics: Interaction with Water and Small Solutes

2005

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“…This latter procedure has previously been shown to be an adequate method to understand the conformational behavior of small peptides. [23][24][25] In the present case, we proceed in a parallel effort by running two molecular dynamics simulations of the peptide soaked in a box of water molecules and using periodic boundary conditions at 300 and 400 K, respectively. The main goal of the present study was to compare the performance of the SA procedure vs. the MD simulations as tools to explore the conformational profile of medium size peptides.…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics

Corcho¹,

Cantó²,

Pérez³

2004

J Comput Chem

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The present study describes an extensive conformational search of substance P using two different computational methods. On the one hand, the peptide was studied using the iterative simulated annealing, and on the other, molecular dynamics simulations at 300 and 400 K. With the former method, the peptide was studied in vacuo with a dielectric constant of 80, whereas using the latter study the peptide was studied in a box of TIP3P water molecules. Analysis of the results obtained using both methodologies was carried out using an in-house methodology using a cluster analysis method based on information theory. Comparison of the two sampling methodologies and the different environment used in the calculations is also analyzed. Finally, the conformational motifs that are characteristic of substance P in a hydrophilic environment are presented and compared with the experimental results available in the literature.

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“…Because of limitations in computer power, these methods have been confined to small molecules such as the pentapeptide enkephalin (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15), the decapeptide gramicidin S (16)(17)(18)(19)(20)(21), and linear fibrous proteins such as collagen-like repeating polytripeptides (22)(23)(24). Inclusion of explicit or implicit hydration in the potential function only exacerbated the global optimization problem.…”

mentioning

confidence: 99%

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

Vila

Ripoll

Scheraga

2003

Proc. Natl. Acad. Sci. U.S.A.

128

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The conformational space of the 10 -55 fragment of the B-domain of staphylococcal protein A has been investigated by using the electrostatically driven Monte Carlo (EDMC) method. The ECEPP͞3 (empirical conformational energy program for peptides) force-field plus two different continuum solvation models, namely SRFOPT (Solvent Radii Fixed with atomic solvation parameters OPTimized) and OONS (Ooi, Oobatake, Né methy, and Scheraga solvation model), were used to describe the conformational energy of the chain. After an exhaustive search, starting from two different random conformations, three of four runs led to native-like conformations. Boltzmann-averaged root-mean-square deviations (RMSD) for all of the backbone heavy atoms with respect to the native structure of 3.35 Å and 4.54 Å were obtained with SRFOPT and OONS, respectively. These results show that the proteinfolding problem can be solved at the atomic detail level by an ab initio procedure, starting from random conformations, with no knowledge except the amino acid sequence. To our knowledge, the results reported here correspond to the largest protein ever folded from a random conformation by an initial-value formulation with a full atomic potential, without resort to knowledge-based information. For many years, methods have been developed to compute the 3D structures of polypeptides, based on empirical atomicbased potential energy functions and global optimization of such functions. Because of limitations in computer power, these methods have been confined to small molecules such as the pentapeptide enkephalin (1-15), the decapeptide gramicidin S (16-21), and linear fibrous proteins such as collagen-like repeating polytripeptides (22-24). Inclusion of explicit or implicit hydration in the potential function only exacerbated the global optimization problem. However, with the recent availability of cost-effective alternatives to large supercomputers, such as Beowulf class cluster computers (25), it is now possible to extend the application of such ab initio physics-based methods to larger molecules.In this article, we report the results of the global optimization of the all-atom force field ECEPP͞3 (empirical conformational energy program for peptides) (26-29) plus two implicit hydration models [SRFOPT (Solvent Radii Fixed with atomic solvation parameters OPTimized; ref. 30) and OONS (Ooi, Oobatake, Némethy, and Scheraga solvation model; ref. 31)], using the electrostatically driven Monte Carlo (EDMC) method (32, 33) to explore the conformational space of the 10-55 fragment of the B-domain of the staphylococcal protein A molecule, efficiently. The structure of this fragment of the B-domain of the protein A molecule is known from x-ray (34) and NMR (35) investigations, and from minimalist and all-atom simulations (36-46). However, such initial-value-formulated simulations (except for ref. 46, which is a boundary-value formulation) were not started from a random conformation. Therefore, in this work, we attempted to provide an extensive exploration of the conf...

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Molecular dynamics simulations of Leu-enkephalin in water and DMSO

Cited by 116 publications

References 52 publications

Protein Surface Dynamics: Interaction with Water and Small Solutes

Protein Surface Dynamics: Interaction with Water and Small Solutes

Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

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