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

Abstract

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 proteins denatured in high-concentration denaturant solution were analyzed by comparing predictions from this method with results from solution X-ray scattering (SXS) measurement. Analysis of the dependence of the mean square radius (Rsq) of protein on the number of residues and the shape of its Kratky profile has confirmed that the highly denaturing solvent serves as a good solvent in accordance with previous reports. It was also found that, in order for a conformational ensemble to reproduce experimental data, the percentage in which main-chain dihedral angles are found in the α region must be in the range of 20-40%. It agrees with studies on the (3)JHNα coupling constant using the multidimensional NMR method. These results confirm that our method for generating diverse conformations of polypeptide chains is very useful to the conformational analysis of unfolded protein, because it enables us to analyze comprehensively both of the local structural features obtained from NMR and the global ones obtained from SXS.

Unexpected trends in the hydrophobicity of fluorinated amino acids reflect competing changes in polarity and conformation

“…Good sampling of the folded protein ensemble can easily be achieved in many cases with molecular dynamics simulations; to sample the unfolded protein ensemble, one can take advantage of a number of algorithms. [87][88][89][90][91] Future work by our group will attempt to extend the solvation model to include mechanisms by which fluorination alters intra-protein non-bonded interactions. This extension is necessary to obtain a complete picture of the mechanisms by which fluorination alters the thermal stability of proteins.…”

Exploring Free-Energy Landscapes of Intrinsically Disordered Proteins at Atomic Resolution Using NMR Spectroscopy

“…One of these descriptions, flexible-meccano (Figure ), , follows these sampling procedures, combined with simple volume exclusion (amino acid-specific hard-spheres placed on the Cβ), to construct statistical ensembles of conformers of unfolded or partially folded proteins, and is used throughout this Review to illustrate expected features of NMR parameters measured in IDPs. Statistical coil descriptions have been developed in this way by a number of different groups, with notably similar potentials covering accessible Ramachandran space (Figure ), ,− divided into four regions αR, αL, βS, and βP. The populations of these regions will be discussed throughout this Review.…”

Unexpected Trends in the Hydrophobicity of Fluorinated Amino Acids Reflect Competing Changes in Polarity and Conformation

“…The model is also directly relevant for proteins: together with short molecular dynamics simulations of proteins in the folded and unfolded ensembles, it can be used to gain insight into how fluorination-induced changes in protein-water interactions contribute to changes in the free energy of folding. Good sampling of the folded protein ensemble can easily be achieved in many cases with molecular dynamics simulations; to sample the un-folded protein ensemble, one can take advantage of a number of algorithms [82][83][84][85][86] . Future work by our group will attempt to extend the solvation model to include mechanisms by which fluorination alters intra-protein non-bonded interactions.…”