Elastic energy of proteins and the stages of protein folding

We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable parameters are fitted to data from the computer simulation of the folding of a set of proteins using the CSAW (conditioned self-avoiding walk) model. The elastic energy gives rise to scaling relations of the form $R_{g}\sim N^{\nu}$ in different regions. It shows three folding stages characterized by the progression with exponents $\nu = 3/5, 3/7, 2/5$, which we identify as the unfolded stage, pre-globule, and molten globule, respectively. The pre-globule goes over to the molten globule via a break in behavior akin to a first-order phase transition, which is initiated by a sudden acceleration of hydrogen bonding

Hierarchical Chain Model of Spider Capture Silk Elasticity

Spider capture silk is a biomaterial with both high strength and high elasticity, but the structural design principle underlying these remarkable properties is still unknown. It was revealed recently by atomic force microscopy that, an exponential force--extension relationship holds both for capture silk mesostructures and for intact capture silk fibers [N. Becker et al., Nature Materials 2, 278 (2003)]. In this Letter a simple hierarchical chain model was proposed to understand and reproduce this striking observation. In the hierarchical chain model, a polymer is composed of many structural motifs which organize into structural modules and supra-modules in a hierarchical manner. Each module in this hierarchy has its own characteristic force. The repetitive patterns in the amino acid sequence of the major flagelliform protein of spider capture silk is in support of this model.Comment: 4 pages, 3 figures. Will be formally published in PR

Effect of photoions on the line shapes of the F\"orster resonance and microwave transitions in cold rubidium Rydberg atoms

Experiments on the spectroscopy of the F\"orster resonance Rb(37P)+Rb(37P) -> Rb(37S)+Rb(38S) and microwave transitions nP -> n'S, n'D between Rydberg states of cold Rb atoms in a magneto-optical trap have been performed. Under ordinary conditions, all spectra exhibited a 2-3 MHz line width independently of the interaction time of atoms with each other or with microwave radiation, although the ultimate resonance width should be defined by the inverse interaction time. Analysis of the experimental conditions has shown that the main source of the line broadening was the inhomogeneous electric field of cold photoions appeared at the excitation of initial Rydberg nP states by broadband pulsed laser radiation. Using an additional pulse of the electric field, which rapidly removed the photoions after the laser pulse, lead to a substantial narrowing of the microwave and F\"orster resonances. An analysis of various sources of the line broadening in cold Rydberg atoms has been conducted.Comment: 10 pages, 6 figure

Energetic Components of Cooperative Protein Folding

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptide-like local conformational restrictions and environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press

Statistical Mechanics of Membrane Protein Conformation: A Homopolymer Model

The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results depending upon membrane permeability and polymer adsorptivity. For a membrane with the permeability larger than a critical value, the integration becomes the second order transition that occurs at the same temperature as that of the adsorption transition. For a nonadsorbing membrane, the integration is of the first order due to the aggregation of $\alpha$-helices.Comment: RevTeX with 5 postscript figure

Searching for New Physics beyond the Standard Model in Electric Dipole Moment

This is a theoretical review of exploration of new physics beyond the Standard Model (SM) in electric dipole moment (EDM) in elementary particles, atoms, and molecule. EDM is a very important CP violating phenomenon and sensitive to new physics. Starting with the estimations of EDM of quarks-leptons in the SM, we explore the new signals beyond the SM. However, these works drive us to more wide fronteers where we serach fundamental physics using atoms and molecules and vice versa. Paramagnetic atoms and molecules have great enhancement factor on electron EDM. Diamagnetic atoms and molecules are very sensitive to nuclear P and T odd processes. Thus the EDM becomes the key word not only of New Physics but also of unprecedented fruitful collaboration among particle, atomic. molecular physics. This review intends to help such collaboration over the wide range of physicists.Comment: 95pages. References are added. Appendix K is revise

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure

A passion for respect: On understanding the role of human needs and morality

In the present paper, we stress the importance of the concept respect in a wide variety of social settings and provide a working definition of this concept by emphasizing how respect relates to the act of communicating full recognition to other people on the dimensions of belongingness and morality. Subsequently, in two separate parts, we discuss why respect is so desired and valued. The first part looks at respect as a means to fulfil important human social concerns (“respect as a means to an end”). The second part looks at the potential moral underpinnings of respect and thus interprets “respect as an end in itself.” Finally, it is suggested that both reasons to value respect explain respect effects as a function of the working selfconcept that is salient (i.e., pragmatic versus idealistic self)

A passion for respect: On understanding the role of human needs and morality

In the present paper, we stress the importance of the concept respect in a wide variety of social settings and provide a working definition of this concept by emphasizing how respect relates to the act of communicating full recognition to other people on the dimensions of belongingness and morality. Subsequently, in two separate parts, we discuss why respect is so desired and valued. The first part looks at respect as a means to fulfil important human social concerns (“respect as a means to an end”). The second part looks at the potential moral underpinnings of respect and thus interprets “respect as an end in itself.” Finally, it is suggested that both reasons to value respect explain respect effects as a function of the working selfconcept that is salient (i.e., pragmatic versus idealistic self)

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

ABSTRACT: A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) aims to collect available data from industry and academia which may be used for this purpose (www.csardock.org). Also, CSAR is charged with organizing community-wide exercises based on the collected data. The first of these exercises was aimed to gauge the overall state of docking and scoring, using a large and diverse data set of protein ligand complexes. Participants were asked to calculate the affinity of the complexes as provided and then recalculate with changes which may improve their specific method. This first data set was selected from existing PDB entries which had binding data (Kd or Ki) in Binding MOAD, augmented with entries from PDBbind. The final data set contains 343 diverse protein ligand complexes and spans 14 pKd. Sixteen proteins have three or more complexes in the data set, from which a user could start an inspection of congeneric series. Inherent experimental error limits the possible correlation between scores and measured affinity; R 2 is limited to ∼0.9 when fitting to the data set without over parametrizing. R 2 is limited to ∼0.8 when scoring the data set with a method trained on outside data. The details of how the data set was initially selected, and the process by which it matured t