Folding of the Protein Domain hbSBD

The folding of the alpha-helice domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to evaluate various thermodynamic parameters defining the equilibrium unfolding, which is well described by the two-state model with the folding temperature T_f = 317.8 K and the enthalpy change Delta H_g = 19.67 kcal/mol. The folding is also studied numerically using the off-lattice coarse-grained Go model and the Langevin dynamics. The obtained results, including the population of the native basin, the free energy landscape as a function of the number of native contacts and the folding kinetics, also suggest that the hbSBD domain is a two-state folder. These results are consistent with the biological function of hbSBD in BCKD.Comment: 25 pages, 7 figures, 1 table, published in Biophysical Journa

Kinetics of the long ssRNA: Steady state

The steady state in the kinetic pathways of the long single-strand RNA (ssRNA) in the approximation of a coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary-structure rearrangement is much longer than that for the formation of the tertiary structure. The entropy and the specific heat of the system as functions of the temperature are calculated and plotted. A non-equilibrium phase transition of the 2nd order has been observed. The possible biological implication of the obtained results is discussed

An enhanced version of SMMP-open-source software package for simulation of proteins

We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192-212]. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. This announcement describes the first major revision of this software package and its newly added features. Title of program:SMMP Catalogue identifier:ADOJ-v2-0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADOJ_v2_0 Program obtainable from: CPC Program Library, Queen\u27s University of Belfast, N. Ireland Operating system under which the program has been tested:LINUX system Programming language used:FORTRAN Computer:PC Pentium Number of lines in distributed program, including test data, etc.:18 492 Number of bytes in distributed program, including test data, etc.:278 995 Distribution format:ASCII Card punching code:ASCII Catalogue Identifier of previous version:ADOJ Journal Reference of previous version:F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192-212 Does the new version supersede the previous version?:Yes Nature of physical problem:Molecular mechanics computations and Monte Carlo simulation of proteins Reasons for the new version:Increased functionality Summary of revisions:Changes in energy function and protein representation; differences in program structure and organization; new functionalities added; miscellaneous changes and additions Method of solution:Utilizes ECEPP2/3 and FLEX potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles Restrictions on the complexity of the problem:The consumed CPU time increases with the size of protein molecule Typical running time:Depends on the size of the molecule under simulation Unusual features of the program:No © 2005 Elsevier B.V. All rights reserved

[SMMP] A modern package for simulation of proteins

A Fortran package is presented which provides useful routines for molecular simulation of proteins within the standard geometry model. Highly efficient algorithms for the calculation of energy and its derivatives are implemented. A set of energy minimization routines and modern Monte Carlo algorithms are added. Three different parameter sets are used to calculate the internal energy: ECEPP/2 potential, ECEPP/3 and the FLEX potential. The solvation energy of the protein can be calculated using the solvent accessible area method. The program is fast and may be successfully exploited even on a single PC. The code is free and open, and can be easily modified. Hence, the package allows researchers and students in a simple and inexpensive way to become familiar with protein simulation techniques, and is especially suitable for lecturers teaching molecular simulation. Yet, when exploited on advanced computers or PC clusters, it is a powerful tool and also valuable for advanced researchers. © 2001 Elsevier Science B.V. All rights reserved

Collapse and hybridization of RNA: View from replica technique approach

The replica technique method is applied to investigate the kinetic behavior of the coarse-grained model for the RNA molecule. A non-equilibrium phase transition of second order between the glassy phase and the ensemble of freely fluctuating structures has been observed. The non-equilibrium steady state is investigated as well and the thermodynamic characteristics of the system have been evaluated. The non-equilibrium behavior of the specific heat is discussed. Based on our analysis, we point out the state in the kinetic pathway in which the RNA molecule is most prone to hybridization