Native geometry and the dynamics of protein folding

In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two dynamical folding regimes depending on the protein chain length. For chains larger than 80 amino acids the folding performance is sensitive to the native state's conformation. Smaller chains, with less than 80 amino acids, fold via two-state kinetics and exhibit a significant correlation between the contact order parameter and the logarithmic folding times. In particular, chains with N=48 amino acids were found to belong to two broad classes of folding, characterized by different cooperativity, depending on the contact order parameter. Preliminary results based on the G\={o} model show that the effect of long range contact interaction strength in the folding kinetics is largely dependent on the native state's geometry.Comment: Proceedings of the BIFI 2004 - I International Conference, Zaragoza (Spain) Biology after the genome: a physical view. To appear in Biophysical Chemistr

ProTherm: Thermodynamic Database for Proteins and Mutants.

The first release of the Thermodynamic Database for Proteins and Mutants (ProTherm) contains more than 3300 data of several thermodynamic parameters for wild type and mutant proteins. Each entry includes numerical data for unfolding Gibbs free energy change, enthalpy change, heat capacity change, transition temperature, activity etc., which are important for understanding the mechanism of protein stability. ProTherm also includes structural information such as secondary structure and solvent accessibility of wild type residues, and experimental methods and other conditions. A WWW interface enables users to search data based on various conditions with different sorting options for outputs. Further, ProTherm is cross-linked with NCBI PUBMED literature database, Protein Mutant Database, Enzyme Code and Protein Data Bank structural database. Moreover, all the mutation sites associated with each PDB structure are automatically mapped and can be directly viewed through 3DinSight developed in our laboratory. The database is available at the URL, http://www.rtc.riken.go.jp/protherm.htm

Scaling behavior of nucleotide cluster in DNA sequences

In this paper we study the scaling behavior of nucleotide cluster in 11 chromosomes of Encephalitozoon cuniculi Genome. The statistical distribution of nucleotide clusters for 11 chromosomes is characterized by the scaling behavior of P(S)∝e(−αS), where S represents nucleotide cluster size. The cluster-size distribution P(S (1)+S (2)) with the total size of sequential C-G cluster and A-T cluster S (1)+S (2) were also studied. P(S (1)+S (2)) follows exponential decay. There does not exist the case of large C-G cluster following large A-T cluster or large A-T cluster following large C-G cluster. We also discuss the relatively random walk length function L(n) and the local compositional complexity of nucleotide sequences based on a new model. These investigations may provide some insight into nucleotide cluster of DNA sequence