Conformational changes in serpins: I. the native and cleaved conformations of α 1 -antitrypsin 1 1Edited by J. M. Thornton

Abstract

The serpins (SERine Proteinase INhibitors) are a family of proteins with important physiological roles, including but not limited to the inhibition of chymotrypsin-like serine proteinases. The inhibitory mechan- ism involves a large conformational change known as the S-->R (stressed-->relaxed) transition. The largest structural differences occur in a region around the scissile bond called the reactive centre loop: In the native (S) state, the reactive centre is exposed, and is free to interact with proteinases. In inhibitory serpins, in the cleaved (R) state the reactive centre loop forms an additional strand within the beta-sheet. The latent state is an uncleaved state in which the intact reactive centre loop is integrated into the A sheet as in the cleaved form, to give an alternative R state. The serpin structures illustrate detailed control of conformation within a single protein. Serpins are also an unusual family of proteins in which homologues have native states with different folding topologies. Determination of the structures of inhibitory serpins in multiple conformational states permits a detailed analysis of the mechanism of the S-->R transition, and of the way in which a single sequence can form two stabilised states of different topology. Here we compare the conformations of alpha(1)-antitrypsin in native and cleaved states. Many protein conformational changes involve relative motions of large rigid subunits. We determine the rigid subunits of alpha(1)-antitrypsin and analyse the changes in their relative position and orientation. Knowing that the conformational change is initiated by cleavage at the reactive centre, we describe a mechanism of the S-->R transition as a logical sequence of mechanical effects, even though the transition likely proceeds in a concerted manner.

Conserved Ser residues, the Shutter Region, and Speciation in Serpin Evolution

“…Ser-53 and Ser-56 are highly conserved residues located in the "shutter" region of the A␤-sheet of the serpin fold ( Fig. 1), which plays a key role in serpin conformational transitions (1,10). Notably, the alignments did not indicate any other positions where a sequence usage dichotomy might serve as an evolutionary marker.…”

“…The shutter is centrally located and lies at the intersection of the major secondary structural elements of the A␤-sheet. Along with the breach, the shutter facilitates sheet opening and accepts the conserved hinge of the reactive center loop, which in turn permits translocation of the protease from one pole of the serpin to the other (10). The evolutionary importance of the shutter in serpin evolution is underscored by the ability of shutter mutations to cause protein malfunctions that result in human disease.…”

SERPINB11 Is a New Noninhibitory Intracellular Serpin

“…Experimental evidence had confirmed the existence of 12 family members, but heretofore data on SERPINB11 was lacking. Moreover, the ability to infer biochemical function based solely on the genomic sequence of SERPINB11 was confounded by the presence of a premature termination codon in exon 4, which, based on known structurefunction relationships, would yield a null mutant in terms of inhibitory activity (42,43). Thus, the goal of this study was to determine whether human SERPINB11 was a pseudogene or a bona fide peptidase inhibitor.…”

“…When we compared the SERPINB11 SNPencoded amino acid variants with those amino acids located at identical positions in four orthologous mammalian genes (mouse, rat, dog, and chimpanzee) and 12 paralogous human clade B genes, conflicts at key positions within hD and hI became apparent. A portion of hD comprises the shutter region, a functional domain that regulates ␤-sheet A movement and permits RSL loop insertion upon peptidase cleavage (42,43,47). The presence of a charged and polar residue at positions 90 and 91, respectively, instead of two hydrophobic residues suggested that these amino acid variants could be contributing to serpin scaffold dysfunction.…”

Characterization and functional analysis of Serp3: a novel myxoma virus-encoded serpin involved in virulence

“…5 B). A structural comparison between the intact and cleaved conformations of α " -antitrypsin suggests that these residues play an important role in controlling conformational changes in serpins (Whisstock et al, 2000). Furthermore, the hinge region (Hopkins et al, 1993) of Serp3 (KTGVDATAFS) is similar to the consensus sequence (EX " GTEAAAX # T, where X " is usually a glutamine or a lysine residue and X # is usually an alanine residue) observed in inhibitory serpins (Fig.…”