title: Molecular dynamics study of Ca(2+) binding loop variants of parvalbumin with modifications at the "gateway" position.
abstract: The helix-loop-helix (i.e. EF-hand) Ca(2+) ion binding motif is characteristic of a large family of high-affinity Ca(2+) ion binding proteins, including the parvalbumins and calmodulins. In this paper we describe a set of molecular dynamics computations on the major parvalbumin from the silver hake (SHPV-B). In all variants examined, both whole protein and fragments thereof, the ninth loop residue in the Ca(2+) binding coordination site in the CD helix-loop-helix region (the so-called "gateway" residue) has been mutated. The three gateway mutations examined are arginine, which has never been found at the gateway position of any EF-hand protein, cysteine, which is the residue observed least in natural EF-hand sites, and serine, which is the most common (by far) non-acidic residue substitution at this position in EF-hand proteins in general, but never in parvalbumins. Results of the molecular dynamics simulations indicate that all three modifications are disruptive to the integrity of the mutated Ca(2+) binding site in the whole parvalbumin protein. In contrast, only the arginine and cysteine mutations are disruptive to the integrity of the mutated Ca(2+) binding site in the CD fragment of the parvalbumin protein. Surprisingly, the serine variant of the CD helix-loop-helix fragment exhibited remarkable stability during the entire molecular dynamics simulation, with retention of the Ca(2+) binding site. These results indicate that there are no inherent problems (for Ca(2+) ion binding) associated with the sequence of the CD helix-loop-helix fragment that precludes the incorporation of serine at the gateway position. Since the CD site is totally disrupted in the whole protein serine variant, this indicates that the Ca(2+) ion binding deficiencies are most likely related to the unique interaction that exists between the paired EF-hands in the whole protein. Our theoretical results correlate well with previous studies on engineered EF-hand proteins and with all of our experimental evidence on the silver hake parvalbumin.
authors: Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA.
authors: K M
authors: KM
authors: Elkins
authors: P Z
authors: PZ
authors: Gatzeva-Topalova
authors: D J
authors: DJ
authors: Nelson
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D001120:Arginine / Q000235:genetics; D001665:Binding Sites; D002104:Cadmium / Q000737:chemistry; D002118:Calcium / Q000737:chemistry; D003198:Computer Simulation; D003545:Cysteine / Q000235:genetics; D020832:EF Hand Motifs; D005399:Fishes; D014644:Genetic Variation; D008956:Models, Chemical; D008958:Models, Molecular; D009154:Mutation; D010320:Parvalbumins / Q000737:chemistry* / Q000235:genetics; D010446:Peptide Fragments / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D020033:Protein Isoforms / Q000737:chemistry; D017434:Protein Structure, Tertiary; D012694:Serine / Q000235:genetics; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D010320:Parvalbumins; D010446:Peptide Fragments; D020033:Protein Isoforms; D002104:Cadmium; D012694:Serine; D001120:Arginine; D003545:Cysteine; D002118:Calcium