Albany 2013: Book of Abstracts
June 11-15 2013
©Adenine Press (2012)
Characterizing the Conformational Space of Two Disordered Peptides in Different Solutions
Amyloid fibrils formed by peptides found in semen have been shown to enhance HIV infectivity in vitro. The first of these peptides to be identified was the 248-286 fragment of prostatic acid phosphatase (PAP248-286) (Munich et at, 2007). PAP248-286 is highly cationic, and its fibrils might facilitate infection by decreasing the electrostatic repulsion between the negatively charged surfaces of the virus and the target cell. Whereas PAP248-286can easily form fibrils in seminal fluid, it needs rapid agitation in other environments, and certain ions have been shown to be critical for its assembly into fibrils (Olsen et al, 2012). However, mutation of the positively charged residues to alanine results in a peptide (PAP248-286 Ala) that can more easily form fibrilar aggregates. We studied PAP248-286 and PAP248-286Ala fibril formation in water and water + NaCl environments. While PAP248-286Ala can efficiently form fibrils in both water and water + NaCl, PAP248-286 can only do so in a water + NaCl solution. The inability of PAP248-286 to form fibrils in water could be due solely to repulsion between the positively charged peptides, an effect that might be diminished by the presence of salt. However, it is also possible that the explanation lies in PAP248-286‘s failure to populate conformations that can easily lead to ordered aggregates. To answer this question, using molecular dynamics simulations, we characterized the ensemble of conformations populated by the two peptides in water and water + NaCl environments. The results indicate that PAP248-286Ala favors contacts that stabilize a strand-turn-strand, or β-arch, motif around P31, the only proline residue in the sequence. Because β-arches are a common feature in amyloid fibrils, and because it is very unlikely that a proline residue would be in any position other than the β-arch, we expect the formation of this motif to be the rate limiting step in PAP248-286 Ala / PAP248-286 fibril formation. Moreover, the contacts stabilizing the β-arch would bring positively charged residues into contact in PAP248-286, which, consistent with the experimental results, would be facilitated by the presence of negative ions. To summarize, we have tried to understand if the inability of PAP248-286 to efficiently form fibrils in water is only due to a slower aggregation caused by electrostatic repulsion between the positively charged peptides. Our data suggest that this effect is also due to electrostatic repulsion between the residues within each monomeric peptide, which prevents PAP248-286 from populating conformations that would lead to ordered aggregates.
This research has been supported by grants from the National Institute of Health (T32AI83206, R21AI094511, T32AI049815 [DE], and P30AI78498)
Olsen JS, DiMaio JTM, Doran TM, Brown C, Nilsson BL, and Dewhurst S, (2012). Seminal Plasma Accelerates Semen-derived Enhancer of Viral Infection (SEVI) Fibril Formation by the Prostatic Acid Phosphatase (PAP(248-286)) Peptide, J. Biol. Chem, 287, 11842-11849.
Ana V. Rojas1
1Department of Biostatistics and Computational Biology