Reading the three-dimensional structure of a protein from its amino acid sequence

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of a protein whose sequence is known. This situation is not particularly satisfactory, in keeping with the fact that while linear sequencing of the amino acids specifying a protein is relatively simple to carry out, the determination of the folded-native-conformation can only be done by an elaborate X-ray diffraction analysis performed on crystals of the protein or, if the protein is very small, by nuclear magnetic resonance techniques. Using insight obtained from lattice model simulations of the folding of small proteins (fewer than 100 residues), in particular of the fact that this phenomenon is essentially controlled by conserved contacts among strongly interacting amino acids, which also stabilize local elementary structures formed early in the folding process and leading to the (post-critical) folding core when they assemble together, we have worked out a successful strategy for reading the three-dimensional structure of a notional protein from its amino acid sequence.Comment: misprints eliminated and small mistakes correcte

A toy model of polymer stretching

We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the cantilever) and long-range interactions terms inside each domain. Exact equilibrium computations and Monte Carlo simulations qualitatively reproduce the experimental saw-tooth pattern of force-extension profiles, corresponding (in our model) to first-order phase transitions. We study the influence of the coupling induced by the cantilever and the pulling speed on the relative heights of the force peaks. The results suggest that the increasing height of the critical force for subsequent unfolding events is an out-of-equilibrium effect due to a finite pulling speed. The dependence of the average unfolding force on the pulling speed is shown to reproduce the experimental logarithmic law.Comment: New revised versio

Design Equation: A Novel Approach to Heteropolymer Design

A novel approach to heteropolymer design is proposed. It is based on the criterion by Kurosky and Deutsch, with which the probability of a target conformation in a conformation space is maximized at low but finite temperature. The key feature of the proposed approach is the use of soft spins (fuzzy monomers) that leads to a design equation, which is an analog of the Boltzmann machine learning equation in the design problem. We implement an algorithm based on the design equation for the generalized HP model on the 3x3x3 cubic lattice and check its performance.Comment: 7 pages, 3 tables, 1 figures, uses jpsj.sty, jpsjbs1.sty, epsf.sty, Submitted to J. Phys. Soc. Jp

Helix Formation and Folding in an Artificial Peptide

We study the relation between $\alpha$-helix formation and folding for a simple artificial peptide, Ala$_{10}$-Gly$_5$-Ala$_{10}$. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. The free-energy landscape of the peptide is evaluated for various temperatures. Our data indicate that folding of this peptide is a two-step process: in a first step two $\alpha$-helices are formed which afterwards re-arrange themselves into a U-like structure.Comment: 15 pages, with 9 eps figure

Fusion of radioactive 132^{132}Sn with 64^{64}Ni

Evaporation residue and fission cross sections of radioactive $^{132}$Sn on $^{64}$Ni were measured near the Coulomb barrier. A large sub-barrier fusion enhancement was observed. Coupled-channel calculations including inelastic excitation of the projectile and target, and neutron transfer are in good agreement with the measured fusion excitation function. When the change in nuclear size and shift in barrier height are accounted for, there is no extra fusion enhancement in $^{132}$Sn+$^{64}$Ni with respect to stable Sn+$^{64}$Ni. A systematic comparison of evaporation residue cross sections for the fusion of even $^{112-124}$Sn and $^{132}$Sn with $^{64}$Ni is presented.Comment: 9 pages, 11 figure