Energy of Hydrogen Bonds Probed by the Adhesion of Functionalized Lipid Layers (original) (raw)
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Effect of hydrogen bonds on protein stability
Arxiv preprint arXiv:1011.3785, 2010
The mechanism of cold-and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density fluctuations of surface water, or the destabilization of hydrophobic contacts because of the displacement of water molecules inside the protein, as proposed for high pressures. However, it is clear that water plays a fundamental role in the process. Here, we review some models that have been proposed to give insight into this problem. Next we describe a coarse-grained model of a water monolayer that successfully reproduces the complex thermodynamics of water and compares well with experiments on proteins at low hydration level. We introduce its extension for a homopolymer in contact with the water monolayer and study it by Monte Carlo simulations. Our goal is to perform a step in the direction of understanding how the interplay of cooperativity of water and interfacial hydrogen bonds affects the protein stability and the unfolding.
The monolayer technique as a tool to study the energetics of protein–protein interactions
Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1998
It this paper, we explore the possibility of using the monolayer technique and hydrophobic homopolypeptides to study the energetics of protein stability. We have studied the stabilization of the bilayer state of poly-L-alanine in its a-helical Ž . Ž . conformation at the air-water interface by measuring compression and expansion surface pressure P -residual area A isotherms at 22 " 28C. The Gibbs free energy of stabilization per alanyl residue transferred from the water exposed state in the monolayer to the inside of the bilayer was calculated from the surface area of the hysteresis loops obtained during compression-expansion cycles performed during the monolayer to bilayer transition. Using atomic solvation parameters and the water accessible surface area per atom group for an alanyl residue in a standard a-helix, we have dissected the free Ž s . energy of stabilization per alanyl residue into the change of solvation free energy DG upon transfer from the water surface to the inside of the bilayer state, and the free energy associated to the formation of hydrophobic van der Waals vdW˚2 Ž . Ž . interactions DG in the bilayer. We estimate a value of 25 " 4 calr mol A for the hydrophobic interaction, as defined s v d W Ž . by the sum of DG and DG per unit of hydrophobic aliphatic accessible surface area in an alanyl residue. q 1998 Elsevier Science B.V.
Potential energy stabilizing a hydrophobic core of protein and its contribution to overall stability
Interaction energy matrix concept is a promising approach to study protein folding, binding and function. The concept of hydrophobic core provides valuable opportunity to unify thermodynamic, kinetic, evolutionary and structural points of view. Method guaranteeing transferable and objective identification of key residues can make possible their further investigations and is the main purpose of this work. The thesis introduces statistical mechanics, molecular modeling and structural biology backgrounds essential for theoretical modeling of the protein folding. Graph representation of proteins in energy space is utilized to characterize energy proportions of sidechains and importance of particular contact types. New definition of contact is proposed and finally, established energy quantities are used to determine residue importance.
Understanding the role of hydrogen bonds in water dynamics and protein stability
Journal of Biological Physics, 2012
The mechanisms of cold and pressure denaturation of proteins are a matter of debate, but it is commonly accepted that water plays a fundamental role in the process. It has been proposed that the denaturation process is related to an increase of hydrogen bonds among hydration water molecules. Other theories suggest that the causes of denaturation are the density fluctuations of surface water, or the destabilization of hydrophobic contacts as a consequence of water molecule inclusions inside the protein, especially at high pressures. We review some theories that have been proposed to give insight into this problem, and we describe a coarse-grained model of water that compares well with experiments for proteins' hydration water. We introduce its extension for a homopolymer in contact with the water monolayer and study it by Monte Carlo simulations in an attempt to understand how the interplay of water cooperativity and interfacial hydrogen bonds affects protein stability.
Journal of Molecular Structure, 2010
Neutron scattering experiments have been used to investigate the effects of temperature and network dimensionality (from hydrated powders to highly concentrated solutions) on the hydrogen bond dynamics of hydration water molecules at specific sites in selected biomolecules. With this aim in view, the evolution of hydration water dynamics of a prototypical hydrophobic amino acid with polar backbone, N-acetyl-leucine-methylamide (NALMA), and a hydrophilic amino acid, N-acetyl-glycine-methylamide (NAGMA), has been investigated as a function of temperature.
The Journal of Physical Chemistry B, 2004
An analysis of the structural and dynamical hydrogen bonding interactions at the lipid water interface from a 10 ns molecular dynamics simulation of a hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer is presented. We find that the average number of hydrogen bonds per lipid oxygen atom varies depending on its position within the lipid. Radial distribution functions are reported for water interacting with lipid oxygen, nitrogen, and phosphorus atoms, as well as for lipid-lipid interactions. The extent of inter-and intramolecular lipid-water-lipid hydrogen bond bridges is explored along with charge pair associations among headgroups of different lipid molecules. We also examine the hydrogen bonding dynamics of water at the lipid surface. A picture emerges of a sticky interface where water that is hydrogen bonded to lipid oxygen atoms diffuses slowly. Hydrogen bonds between water and the double bonded lipid oxygen atoms are longer lived than those to single bonded lipid oxygen atoms, and hydrogen bonds between water and the tail lipid oxygen atoms are longer lived than those to headgroup oxygen atoms. The implications of these results for lateral proton transfer at the interface are also discussed.
Contribution of hydrogen bonds to protein stability
Protein Science, 2014
Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, D(DG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A. The structures are very similar to wild type RNase Sa and the hydrogen bonding partners form intermolecular hydrogen bonds to water in all three mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions. (1) Hydrogen bonds contribute favorably to protein stability. The contribution of hydrogen bonds to protein stability is strongly context dependent. (3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. (5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein.
Current Opinion in Colloid & Interface Science, 2011
A water molecule in the vicinity of a hydrophobic surface forms fewer and energetically altered hydrogen bonds compared to a bulk molecule because the hydrophobic surface restricts the space available for other water molecules necessary for its hydrogen bonding. In this vicinity, the number of hydrogen bonds per water molecule depends on its distance to the surface and its orientation. We review recent advances in analytic models of water hydrogen bonding and of its role in hydrophobic hydration and hydrophobic interactions with the emphasis on the models providing the number of hydrogen bonds per liquid water molecule as a function of its distance to a hydrophobic surface. The first such model [Luzar A, Svetina S, Zeks B. J Chem Phys. 1985;82:5146-54] was based on two reference quantities: energy of a hydrogen bond and ratio of number of broken and formed bonds, both in the vicinity of the surface. In the recent, probabilistic hydrogen bond model [Djikaev YS, Ruckenstein E. J Chem Phys. 2010; 133: doi:10.1063/1.3499318.] the number of hydrogen bonds per bulk water molecule serves as a single reference to obtain an analytic expression for this dependence (the number of hydrogen bonds per water molecule vs its distance to a hydrophobic surface). This function can be used to develop analytic models for the role of hydrogen bonding in the hydration of hydrophobic particles and their solvent-mediated interaction and to examine the temperature effects on these phenomena.