A New Efficient Method for Generating Conformations of Unfolded Proteins with Diverse Main-Chain Dihedral-Angle Distributions.

A new method for generating polypeptide-chain conformations has been developed for studying structural characteristics of unfolded proteins. It enables us to generate a large number of conformations very rapidly by avoiding atomic collisions efficiently with the use of main-chain dihedral-angle distributions derived from a crystal-structure database of proteins. In addition, combining main-chain dihedral-angle distributions for the amino acid residues incorporated in different secondary structures, we can obtain diverse conformational ensembles with different structural features.

Structural characteristics of hydration sites in lysozyme.

A new method is presented for determining the hydration site of proteins, where the effect of structural fluctuations in both protein and hydration water is explicitly considered by using molecular dynamics simulation (MDS). The whole hydration sites (HS) of lysozyme are composed of 195 single HSs and 38 clustered ones (CHS), and divided into 231 external HSs (EHS) and 2 internal ones (IHS). The largest CHSs, 'Hg' and 'Lβ', are the IHSs having 2.

Global structure analysis of acid-unfolded myoglobin with consideration to effects of intermolecular coulomb repulsion on solution X-ray scattering.

To obtain information on the global structure of protein in the acid-unfolded (AU) state, the structure of apomyoglobin (apoMb) was analyzed by using the solution X-ray scattering (SXS) method. SXS profiles were obtained over a wide range of protein concentrations, 1-18 mg mL-1, under strongly acidic conditions. From analysis of the SXS profile extrapolated to a zero protein concentration, the mean square radius, Rsq, of AU-apoMb at 20 mM HCl was estimated to be 4.

Mutational analysis of protein solubility enhancement using short peptide tags.

Protein aggregation is a common phenomenon. The preparation of highly concentrated protein samples, typically required for biophysical measurements, often involves a time consuming and tedious testing of solvent conditions for improving protein solubility. Here, in a systematic analysis, we have determined the increase in solubility upon the addition of SEP-tags (solubility enhancement peptide tags) containing, one, three, and five lysines or arginines (or six arginines) to either the N or C terminus of our low solubility model protein, bovine pancreatic trypsin inhibitor variant, BPTI-22 (a BPTI variant containing 22 alanines).

Evaluation of intrinsic compressibility of proteins by molecular dynamics simulation.

Molecular dynamics simulation has been performed on five native proteins in water to evaluate their intrinsic isothermal compressibilities beta(T,int). To identify physical factors contributing to protein compressibility, a general method is presented for analyzing the compressibility of mechanically inhomogeneous systems. The value of beta(T,int) varies with protein species considerably: beta-lactoglobulin (14.

Structural stability and solution structure of chaperonin GroES heptamer studied by synchrotron small-angle X-ray scattering.

The GroES protein from Escherichia coli is a well-known member of the molecular chaperones. GroES consists of seven identical 10 kDa subunits, and forms a dome-like oligomeric structure. In order to obtain information on the structural stability and unfolding-refolding mechanism of GroES protein, especially at protein concentrations (0.

Contribution of solvent water to the solution X-ray scattering profile of proteins.

A theoretical framework is presented to analyze how solvent water contributes to the X-ray scattering profile of protein solution. Molecular dynamics simulations were carried out on pure water and an aqueous solution of myoglobin to determine the spatial distribution of water molecules in each of them. Their solution X-ray scattering (SXS) profiles were numerically evaluated with obtained atomic-coordinate data.