MARTIN Osvaldo Antonio
Accounting for a mirror-image conformation as a subtle effect in protein folding
KACHLISHVILI, KHATUNA; MAISURADZE, GIA G. ; MARTÍN OSVALDO A.; LIWO, ADAM; VILA, JORGE A.; SCHERAGA, HAROLD A.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
NATL ACAD SCIENCES
Lugar: Washington DC, USA; Año: 2014 vol. 111 p. 8458 - 8463
By using local (free-energy profiles along the amino acid sequence and 13Cα chemical shifts) and global (principal component) analyses to examine the molecular dynamics of protein-folding trajectories, generated with the coarse-grained united-residue force field, for the B domain of staphylococcal protein A, we are able to (i) provide the main reason for formation of the mirror-image conformation of this protein, namely, a slow formation of the second loop and part of the third helix (Asp29?Asn35), caused by the presence of multiple local conformational states in this portion of the protein; (ii) show that formation of the mirror-image topology is a subtle effect resulting from local interactions; (iii) provide a mechanism for how protein A overcomes the barrier between the metastable mirror-image state and the native state; and (iv)offer a plausible reason to explain why protein A does not remain in the metastable mirror-image state even though the mirror-image and native conformations are at least energetically compatible