Solvation: A Molecular Dynamics Study of a Dipeptide in Water

Karplus, Martin; Rossky, Peter J.

doi:10.1021/bk-1980-0127.ch002

Cited by 11 publications

(7 citation statements)

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“…Our results demonstrate an increased short-time mobility of waters near the hydrophobic patches, rooted in nondiffusive motion. Other authors have reported an effect of hydrophobicity on the diffusive motion relative to polar residues, but there is disagreement on whether hydrophobic surfaces increase (Levitt and Sharon, 1988) or decrease (Karplus and Rossky, 1980;Brooks and Karplus, 1989) the diffusion coefficient. Clearly, the disagreement between the computational studies suggests that the simulation of the physical properties of water at a protein surface are modeldependent because of limitations of the various protein and water force fields.…”

Section: Discussionmentioning

confidence: 98%

Structure and Dynamics of Calmodulin in Solution

Wriggers

Mehler

Pitici

et al. 1998

Biophysical Journal

147

158

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To characterize the dynamic behavior of calmodulin in solution, we have carried out molecular dynamics (MD) simulations of the Ca2+-loaded structure. The crystal structure of calmodulin was placed in a solvent sphere of radius 44 A, and 6 Cl- and 22 Na+ ions were included to neutralize the system and to model a 150 mM salt concentration. The total number of atoms was 32,867. During the 3-ns simulation, the structure exhibits large conformational changes on the nanosecond time scale. The central alpha-helix, which has been shown to unwind locally upon binding of calmodulin to target proteins, bends and unwinds near residue Arg74. We interpret this result as a preparative step in the more extensive structural transition observed in the "flexible linker" region 74-82 of the central helix upon complex formation. The major structural change is a reorientation of the two Ca2+-binding domains with respect to each other and a rearrangement of alpha-helices in the N-terminus domain that makes the hydrophobic target peptide binding site more accessible. This structural rearrangement brings the domains to a more favorable position for target binding, poised to achieve the orientation observed in the complex of calmodulin with myosin light-chain kinase. Analysis of solvent structure reveals an inhomogeneity in the mobility of water in the vicinity of the protein, which is attributable to the hydrophobic effect exerted by calmodulin's binding sites for target peptides.

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Section: Discussionmentioning

confidence: 98%

Structure and Dynamics of Calmodulin in Solution

Wriggers

Mehler

Pitici

et al. 1998

Biophysical Journal

147

158

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“…The statistically preferred orientation of /, water molecules adjacent to anionic kosmotropes is with the water hydrogen atom approximately on a straight line between the anionic kosmotrope and the water oxygen (133, 402); the statistically preferred orientation of /, water molecules adjacent to cationic kosmotropes, although not known with certainty, is probably with a water oxygen unshared electron pair approximately on a straight line between the cationic kosmotrope and the water oxygen (133, 229,828). The statistically preferred orientation of /; water molecules adjacent to non-polar kosmotropes is with 1 hydrogen bond or unshared electron pair approximately perpendicular to and pointing away from the surface of the solute (402,(463)(464)746). The double-headed arrow indicates maximization of hydrogen-bonding interactions approximately parallel to the surface of the test solute; this surface may be curved, as in clathrate structures (170,171,289,445,842).…”

Section: A Molecular Model For the Structure Of Water At Interfacmentioning

confidence: 98%

“…The angle dependent H-bond interaction determines about § of the intermolecular energy of u -6 kcal/mol in ice (480,565), and we shall present a qualitative picture of the behaviour of liquid water primarily in terms of hydrogen-bonding interactions. We assume that each of the water molecules in the first surface layer at the air-water interface makes slightly fewer hydrogen bonds with its neighbours than the 3-45 typical for bulk water at 30 °C (463)(464)746). We suggest that the rapidly rotating water molecules in the first surface layer will show a slight preference for orientations in which they are net hydrogen bond donors (Lewis acid (450) centres) to the bulk solution.…”

Section: A Molecular Mechanism For the Origins Of H O F M E I S mentioning

confidence: 99%

The Hofmeister effect and the behaviour of water at interfaces

Collins

Washabaugh

1985

Quart. Rev. Biophys.

1,534

1,455

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Starting from known properties of non-specific salt effects on the surface tension at an air-water interface, we propose the first general, detailed qualitative molecular mechanism for the origins of ion-specific (Hofmeister) effects on the surface potential difference at an air-water interface; this mechanism suggests a simple model for the behaviour of water at all interfaces (including water-solute interfaces), regardless of whether the non-aqueous component is neutral or charged, polar or non-polar. Specifically, water near an isolated interface is conceptually divided into three layers, each layer being I water-molecule thick. We propose that the solute determines the behaviour of the adjacent first interfacial water layer (I1); that the bulk solution determines the behaviour of the third interfacial water layer (I3), and that both I1 and I3 compete for hydrogen-bonding interactions with the intervening water layer (I2), which can be thought of as a transition layer. The model requires that a polar kosmotrope (polar water-structure maker) interact with I1 more strongly than would bulk water in its place; that a chaotrope (water-structure breaker) interact with I1 somewhat less strongly than would bulk water in its place; and that a non-polar kosmotrope (non-polar water-structure maker) interact with I1 much less strongly than would bulk water in its place. We introduce two simple new postulates to describe the behaviour of I1 water molecules in aqueous solution. The first, the 'relative competition' postulate, states that an I1 water molecule, in maximizing its free energy (--delta G), will favour those of its highly directional polar (hydrogen-bonding) interactions with its immediate neighbours for which the maximum pairwise enthalpy of interaction (--delta H) is greatest; that is, it will favour the strongest interactions. We describe such behaviour as 'compliant', since an I1 water molecule will continually adjust its position to maximize these strong interactions. Its behaviour towards its remaining immediate neighbours, with whom it interacts relatively weakly (but still favourably), we describe as 'recalcitrant', since it will be unable to adjust its position to maximize simultaneously these interactions.(ABSTRACT TRUNCATED AT 400 WORDS)

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“…(There are, however, faster low‐resolution models that achieve good results9). Other approaches try to identify flexible hinge joints or rigid domains directly from a single conformation of the molecule 10–14. Very recently, an ingenious and elegant approach was developed for estimating the flexibility of proteins using graph theory 14.…”

Section: Introductionmentioning

confidence: 99%

Predictions of protein flexibility: First‐order measures

2004

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The normal modes of a molecule are utilized, in conjunction with classical conformal vector field theory, to define a function that measures the capability of the molecule to deform at each of its residues. An efficient algorithm is presented to calculate the local chain deformability from the set of normal modes of vibration. This is done by considering each mode as an off-grid sample of a deformation vector field. Predictions of deformability are compared with experimental data in the form of dihedral angle differences between two conformations of ten kinases by using a modified correlation function. Deformability calculations correlate well with experimental results and validate the applicability of this method to protein flexibility predictions. Proteins 2004;56:661-668.

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Solvation: A Molecular Dynamics Study of a Dipeptide in Water

Cited by 11 publications

References 0 publications

Structure and Dynamics of Calmodulin in Solution

Structure and Dynamics of Calmodulin in Solution

The Hofmeister effect and the behaviour of water at interfaces

Predictions of protein flexibility: First‐order measures

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