Six "cavity-creating" mutants, Leu46----Ala (L46A), L99A, L118A, L121A, L133A, and Phe153----Ala (F153A), were constructed within the hydrophobic core of phage T4 lysozyme. The substitutions decreased the stability of the protein at pH 3.0 by different amounts, ranging from 2.7 kilocalories per mole (kcal mol-1) for L46A and L121A to 5.0 kcal mol-1 for L99A. The double mutant L99A/F153A was also constructed and decreased in stability by 8.3 kcal mol-1. The x-ray structures of all of the variants were determined at high resolution. In every case, removal of the wild-type side chain allowed some of the surrounding atoms to move toward the vacated space but a cavity always remained, which ranged in volume from 24 cubic angstroms (A3) for L46A to 150 A3 for L99A. No solvent molecules were observed in any of these cavities. The destabilization of the mutant Leu----Ala proteins relative to wild type can be approximated by a constant term (approximately 2.0 kcal mol-1) plus a term that increases in proportion to the size of the cavity. The constant term is approximately equal to the transfer free energy of leucine relative to alanine as determined from partitioning between aqueous and organic solvents. The energy term that increases with the size of the cavity can be expressed either in terms of the cavity volume (24 to 33 cal mol-1 A-3) or in terms of the cavity surface area (20 cal mol-1 A-2). The results suggest how to reconcile a number of conflicting reports concerning the strength of the hydrophobic effect in proteins.

The propensity of an amino acid to form an alpha helix in a protein was determined by multiple amino substitutions at positions 44 and 131 in T4 lysozyme. These positions are solvent-exposed sites within the alpha helices that comprise, respectively, residues 39 to 50 and 126 to 134. Except for two acidic substitutions that may be involved in salt bridges, the changes in stability at the two sites agree well. The stability values also agree with those observed for corresponding amino acid substitutions in some model peptides. Thus, helix propensity values derived from model peptides can be applicable to proteins. Among the 20 naturally occurring amino acids, proline, glycine, and alanine each have a structurally unique feature that helps to explain their low or high helix propensities. For the remaining 17 amino acids, it appears that the side chain hydrophobic surface buried against the side of the helix contributes substantially to alpha helix propensity.

Serine proteinases like thrombin can signal to cells by the cleavage/activation of proteinase-activated receptors (PARs).Although thrombin is a recognized physiological activator of PAR 1 and PAR 4 , the endogenous enzymes responsible for activating PAR 2 in settings other than the gastrointestinal system, where trypsin can activate PAR 2 , are unknown. We tested the hypothesis that the human tissue kallikrein (hK) family of proteinases regulates PAR signaling by using the following: 1) a high pressure liquid chromatography (HPLC)-mass spectral analysis of the cleavage products yielded upon incubation of hK5, -6, and -14 with synthetic PAR N-terminal peptide sequences representing the cleavage/activation motifs of PAR 1 , PAR 2 , and PAR 4 ; 2) PAR-dependent calcium signaling responses in cells expressing PAR 1 , PAR 2 , and PAR 4 and in human platelets; 3) a vascular ring vasorelaxation assay; and 4) a PAR 4 -dependent rat and human platelet aggregation assay. We found that hK5, -6, and -14 all yielded PAR peptide cleavage sequences consistent with either receptor activation or inactivation/disarming. Furthermore, hK14 was able to activate PAR 1 , PAR 2 , and PAR 4 and to disarm/inhibit PAR 1 . Although hK5 and -6 were also able to activate PAR 2 , they failed to cause PAR 4 -dependent aggregation of rat and human platelets, although hK14 did. Furthermore, the relative potencies and maximum effects of hK14 and -6 to activate PAR 2 -mediated calcium signaling differed. Our data indicate that in physiological settings, hKs may represent important endogenous regulators of the PARs and that different hKs can have differential actions on PAR 1 , PAR 2 , and PAR 4 . Proteinase-activated receptors (PAR 1-4 )3 compose a unique family of four G-protein-coupled cell surface receptors for certain proteinases (1-9). Proteolytic cleavage within the extracellular N terminus reveals a tethered ligand that binds to the extracellular receptor domains to initiate cell signaling (5, 6, 9, 10). Proteinases that activate PARs include coagulation factors, enzymes from inflammatory cells, and proteinases from epithelial cells and neurons. These enzymes, generated and released during injury and inflammation, can cleave and activate PARs on many cell types from a variety of species (humans, rats, and mice) to regulate the critically important processes of hemostasis, inflammation, pain, and tissue repair. Other proteinases that cleave PARs downstream of the N-terminal tethered ligand sequence disable the receptors for further proteolytic activation, thus abrogating PAR signaling. It is of considerable interest to identify the proteinases that activate and/or disable PARs, in view of the emerging role that these receptors can play in diseases such as asthma, arthritis, inflammatory bowel disease, and cancer (5-7).In some systems, the proteinases that activate PARs have been established. For example, in the circulatory system, PAR 1 , PAR 3 , and PAR 4 are recognized physiological targets for thrombin (4), which does not efficiently acti...

We have identified a novel serine protease, myelencephalon-specific protease (MSP), which is preferentially expressed in the adult CNS, and therein, is abundant in both neurones and oligodendroglia. To determine the potential activity of MSP in CNS demyelination, we examined its expression in multiple sclerosis lesions and in two animal models of multiple sclerosis: Theiler's murine encephalomyelitis virus (TMEV) and myelin oligodendrocyte glycoprotein (MOG)-induced experimental allergic encephalomyelitis (EAE) in marmosets. High levels of MSP were present within infiltrating mononuclear cells, including macrophages and T cells, which characteristically fill sites of demyelination, both in multiple sclerosis lesions and in animal models of this disease. The functional consequence of excess MSP on oligodendroglia was determined in vitro by evaluating the effects of recombinant MSP (r-MSP) on oligodendrocyte survival and process number. Application of excess r-MSP resulted in a dramatic loss of processes from differentiated oligodendrocytes, and a parallel decrease in process outgrowth from immature cells. Transfection of oligodendrocyte progenitors with an MSP-green fluorescent protein construct produced similar changes in oligodendrocyte process number. Importantly, r-MSP did not affect oligodendrocyte survival or differentiation towards the sulphatide-positive lineage. We further demonstrate that myelin basic protein, and to a lesser extent myelin oligodendrocyte glycoprotein, can serve as MSP substrates. These studies support the hypothesis that excess MSP, as is present in inflammatory CNS lesions, promotes demyelination.

The human kallikreins are a large multigene family of closely related serine-type proteases. In this regard, they are similar to the multigene kallikrein families characterized in mice and rats. There is a much more extensive body of knowledge regarding the function of mouse and rat kallikreins in comparison with the human kallikreins. Human kallikrein 6 has been proposed as the homologue to rat myelencephalon-specific protease, an arginine-specific degradative-type protease abundantly expressed in the central nervous system and implicated in demyelinating disease. We present the xray crystal structure of mature, active recombinant human kallikrein 6 at 1.75-Å resolution. This high resolution model provides the first three-dimensional view of one of the human kallikreins and one of only a few structures of serine proteases predominantly expressed in the central nervous system. Enzymatic data are presented that support the identification of human kallikrein 6 as the functional homologue of rat myelencephalon-specific protease and are corroborated by a molecular phylogenetic analysis. Furthermore, the xray data provide support for the characterization of human kallikrein 6 as a degradative protease with structural features more similar to trypsin than the regulatory kallikreins.Recent studies demonstrate that humans have a large multigene family of at least 15 different kallikreins (serine type proteases, abbreviated as KLK 1 in reference to the gene, or hK in reference to the protein) (1). Similarly, the mouse and rat kallikrein gene families are characterized by a large number of closely related members that presumably arose because of gene duplication events (2-6). The different members of the mouse and rat kallikreins are characterized by a high degree of amino acid identity, but typically exhibit different preferences toward peptide substrates (7-12). Several human kallikreins have been identified as potentially useful diagnostic markers for breast (KLK3 and KLK6), prostate (KLK2 and KLK3), and ovarian (KLK6, KLK9, KLK10, and KLK11) cancers as well as neurodegenerative diseases such as Alzheimer's (KLK6) (1, 13-17).Myelencephalon-specific protease (MSP) is a member of the rat kallikrein gene family that is abundantly expressed in the rodent central nervous system and shown to be up-regulated in response to glutamate receptor-mediated excitotoxic injury (18). Potential human homologues to rat MSP have also been identified (18) and have been alternatively named protease M (19), Zyme (20), and neurosin (21). Mouse homologues to MSP have been reported as brain and skin serine protease (BSSP) (22) and brain serine protease (BSP) (23). It has been postulated that MSP/protease M/neurosin may play a key role in the regulation of myelin turnover and in demyelinating disease (18, 24 -27), including the development of multiple sclerosis lesions (25). Furthermore, this kallikrein may also play a role in the degradation of ␤-amyloid or turnover of amyloid precursor protein (28,29). The kinetic properties of MSP have ident...

Fibroblast growth factors (FGFs) are mitogenic and chemotactic agents for a wide variety of cell types and play a primary role in the regulation of angiogenesis. Angiogenesis is involved in a variety of critical physiological events including organogenesis, wound healing, ischemic collateral circulation, and solid tumor growth. High-resolution structural information is key to understanding the mechanism of action of these growth factors. We report here the X-ray crystal structure of human acidic FGF (aFGF), with data extending to 2.0 Å resolution. The crystal contains four independent molecules in the asymmetric unit. Each molecule contains a single bound sulfate ion, in similar juxtapositions. The bound sulfate is stabilized through hydrogen-bond interactions with residues Asn 18, Lys 113, and Lys 118 and defines a potential heparin binding site. The hydrogen bond with the Nδ 2 moiety of Asn 18 appears to be the most conserved interaction, being similar to those observed for sulfate ion bound to human basic FGF (bFGF) and similar but not identical to interactions observed for bovine aFGF with heparin analogs. Of the added solvent groups, five ordered water molecules are conserved in each of the four independent structures of human aFGF. These water molecules, located at buried positions, provide hydrogen bonding partnerships with several buried polar groups in the core of the protein. A central interior cavity exists in each of the four structures, with sizes ranging from approximately 20 to 50 Å 3 . The cavity sizes appear to be significantly smaller than that observed in the related protein interleukin-1 . The region comprising the high affinity FGF receptor binding site is structurally very similar to the corresponding region from human bFGF, whereas the low affinity site is structurally quite different. The results provide a structural basis for the role of the low affinity binding site in FGF receptor discrimination.

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The majority of protein architectures exhibit elements of structural symmetry, and "gene duplication and fusion" is the evolutionary mechanism generally hypothesized to be responsible for their emergence from simple peptide motifs. Despite the central importance of the gene duplication and fusion hypothesis, experimental support for a plausible evolutionary pathway for a specific protein architecture has yet to be effectively demonstrated. To address this question, a unique "top-down symmetric deconstruction" strategy was utilized to successfully identify a simple peptide motif capable of recapitulating, via gene duplication and fusion processes, a symmetric protein architecture (the threefold symmetric β-trefoil fold). The folding properties of intermediary forms in this deconstruction agree precisely with a previously proposed "conserved architecture" model for symmetric protein evolution. Furthermore, a route through foldable sequence-space between the simple peptide motif and extant protein fold is demonstrated. These results provide compelling experimental support for a plausible evolutionary pathway of symmetric protein architecture via gene duplication and fusion processes.protein design | protein folding | protein symmetry