The Vma21p protein in yeast is an essential assembly chaperone for the vacuolar ATPase, the major proton pump of cellular membranes. In this issue, Ramachandran et al. (2009) report that mutations in the gene encoding the human homolog VMA21 cause the disease X-linked myopathy with excessive autophagy through an unexpected mechanism.

Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of prote...

Analysis of the relationship between surface accessibility and amino acid conservation in multiple sequence alignments of homologous proteins confirms expected trends for hydrophobic amino acids, but reveals an unexpected difference between the conservation of Asp, Glu and Gln. Even when not in an active site, Asp is more highly conserved than Glu. There is a clear preference for conserved and ...

MOTIVATION The problem of early-stage protein folding is critical for protein structure prediction. The model presented introduces a common definition of protein structures which may be treated as the possible in silico early-stage form of the polypeptide chain. Limitation of the conformational space to the ellipse path on the Ramachandran map was tested as a possible sub-space to represent the...

Reasons for the formation of extended-strands (E-strands) in proteins are often associated with the formation of beta-sheets. However E-strands, not part of beta-sheets, commonly occur in proteins. This raises questions about the structural role and stability of such isolated E-strands. Using a dataset of 250 largely non-homologous and high-resolution (<2 A) crystal structures of proteins, we h...

2 Iron Cluster 3 G. L. Gutsev,*,† C. A. Weatherford,† P. Jena,‡ E. Johnson, and B. R. Ramachandran 4 †Department of Physics, Florida A&M University, Tallahassee, Florida 32307, United States 5 ‡Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States 6 Environmental Sciences Institute, Florida A&M University, Tallahassee, Florida 32307, United States 7 Co...