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At least 1,243 records · Page 69Linked to original sources
PubMed2006

Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes.

Entropic and enthalpic contributions to the hydrophobic interaction between nanoscopic hydrophobic solutes, modeled as graphene plates in water, have been calculated using molecular dynamics simulations in the isothermal-isobaric (NPT) ensemble with free energy perturbation methodology. We find the stabilizing contribution to the free energy of association (contact pair formation) to be the favorable entropic part, the enthalpic contribution being highly unfavorable. The desolvation barrier is dominated by the unfavorable enthalpic contribution, despite a fairly large favorable entropic compensation. The enthalpic contributions, incorporating the Lennard-Jones solute-solvent terms, largely determine the stability of the solvent separated configuration. We decompose the enthalpy into a direct solute-solute term, the solute-solvent interactions, and the remainder that contains pressure-volume work as well as contributions due to solvent reorganization. The enthalpic contribution due to changes in water-water interactions arising from solvent reorganization around the solute molecules is shown to have major contribution in the solvent induced enthalpy change.

Algorithms↗
PubMed1998

The polymer basis of kinetics and equilibria of enzymes: the accessible-volume origin of entropy changes in a class Abeta-lactamase.

The occurrence of enzymatic catalysis, as for any chemical reaction, depends critically upon close contact of the reactants, since making/breaking of bonds occurs over distances of about 0.2 A. Unlike small molecules, each enzyme molecule acts as an ordered solvent and reactant. Each group important to the enzyme reaction interacts with the substrate, then moves away, and subsequently binds another substrate. In other words, the group undergoes round trips in structure. For a round trip, the thermochemical state functions deltaG, deltaH, deltaS, etc., are zero. As a consequence, control of the binding of substrate must reside in the nonbinding conformations of the polymer since they govern the different fractions of time the macromolecule is in the correct conformation for bonding. Applying standard macromolecular models to the enzymes suggests that the majority of free energy for an enzyme reaction resides in the enzyme structure as an entropic contribution. Enthalpic contributions come from bond formation with the substrates and substrate structural changes. Further, it is shown that the molecular mechanisms that can effect binding and allosteric control fall into only three classes. Three x-ray structures of class A beta-lactamases (native, mutant, and with substrate) show the individual binding groups at the active site change their accessible volumes depending on substrate binding and mutant form. From these volume differences, the deltaS of reaction is calculated. The x-ray-derived deltaG = - TdeltaS matches the deltaG = -RT ln k1 from changes in rate constants for the same set of beta-penicillinases.

Entropy↗
PubMed2005

Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes.

Coarse-grained models have been extremely valuable in promoting our understanding of protein folding. However, the quantitative accuracy of existing simplified models is strongly hindered either from the complete removal of frustration (as in the widely used Gō-like models) or from the compromise with the minimal frustration principle and/or realistic protein geometry (as in the simple on-lattice models). We present a coarse-grained model that "naturally" incorporates sequence details and energetic frustration into an overall minimally frustrated folding landscape. The model is coupled with an optimization procedure to design the parameters of the protein Hamiltonian to fold into a desired native structure. The application to the study of src-Src homology 3 domain shows that this coarse-grained model contains the main physical-chemical ingredients that are responsible for shaping the folding landscape of this protein. The results illustrate the importance of nonnative interactions and energetic heterogeneity for a quantitative characterization of folding mechanisms.

Entropy↗
PubMed2005

[Validation of an entropy-based algorithm for registration of serial 3D MR mammography data].

The aim of this study was to develop and implement an algorithm for the co-registration of 3D breast MRI sets acquired at two slightly different patient positions (repetitive examination). Combined translation and rotation with locally varying parameters were applied for the purpose of coordinate transformation. A phantom allowing selective changes of the volume of the glandular tissue model was developed, in order to prove the robustness of the proposed matcher against local changes. Serial 3D data sets of phantoms and volunteers were acquired to validate the routines. Co-registration was performed using mutual information (MI) as a similarity measure of the matching of the acquired images. In the phantom study, the phantom was deliberately shifted and rotated around horizontal and vertical axes. Starting the registration with global translations using a rigid matcher, the horizontal (phi) and vertical (theta) rotation angles were optimized in an iteration loop for each slice. This method was then applied to the breast data sets. Application of the algorithm on serial 3D MR data sets improved the co-registration especially in consideration of varying local tissue volumes. The algorithm represents a compromise between a pure rigid and an elastic 3D matcher.

Algorithms↗
PubMed2001

Entropy and local uncertainty of data from sensory neurons.

We present an empirical comparison between neural interspike interval sequences obtained from two different kinds of sensory receptors. Both differ in their internal structure as well as in the strength of correlations and the degree of predictability found in the respective spike trains. As a further tool in this context, we suggest the local uncertainty, assigning a well-defined predictability to individual spikes. The local uncertainty is demonstrated to reveal significant patterns within the interspike interval sequences, even when its overall structure is (almost) random. Our approach is based on the concept of symbolic dynamics and information theory.

Animals↗
PubMed2002

Configurational entropy and mechanical properties of cross-linked polymer chains: implications for protein and RNA folding.

We discuss the statistical mechanical properties of a single polymer chain that forms cross links among its monomers. Models of this type have served as prototypes in theories of RNA and protein folding. The chain is allowed to form pseudoknots and its monomers can each participate in multiple cross links. We demonstrate that the conformational free energy of such a chain can be estimated by using an algorithm that scales as a power of the number of cross links N(N1-N3, depending on the problem). Straightforward exact evaluation of the chain partition function via multidimensional integration scales exponentially with N and often is computationally prohibitive. Our approach can also be used to compute the "entropic force" generated by a cross-linked chain when it is stretched at its ends. Such forces can be directly measured by atomic force microscopy or by laser optical trap experiments performed on single RNA, DNA, and protein molecules.

Biomechanical Phenomena↗