Active site and exosite binding of alpha-thrombin

alpha-thrombin possesses at least three independent binding sites for substrate, inhibitor and effector molecules. The S1 subsite of the active site is specific for an arginine side group while S2 is a more extended apolar site. The fibrinogen recognition exosite, which usually operates in concert with catalysis, appears to circumnavigate about a third of the surface, although evidence suggests that recognition of a tetra- or pentapeptide sequence is sufficient. Another highly electropositive region of thrombin, which binds the second kringle of prothrombin through salt bridges, is also most likely the heparin binding site. All three sites display distinct binding modes with different molecules. In the active site, these can arise from different optical enantiomorphs combined with reversal of main chain direction, while in the fibrinogen anion binding exosite, certain peptide side chains (hydrophobic) are tolerated of imprecision or are not relevant for binding or undergo a conformational change in substrate binding. Such apparently indiscriminant behaviour easily accounts for the diversity of thrombin functions at the molecular level.

Structure of the hirulog 3-thrombin complex and nature of the S' subsites of substrates and inhibitors

The X-ray crystallographic structure of the human alpha-thrombin complex with hirulog 3 (a potent, noncleavable hirudin-based peptide of the "hirulog" class containing a beta-homoarginine at the scissile bond), which is isomorphous with that of the hirugen-thrombin crystal structure, was solved at 2.3-A resolution by starting with a model for thrombin derived from the hirugen-thrombin complex and was refined by restrained least squares methods (R = 0.132). Residues of hirulog 3 were well-defined in the electron density, which included most of the pentaglycine linker and the C-terminal helical turn that was disordered in a related structure of thrombin with hirulog 1. The interactions of D-Phe1'-Pro2'-beta-homoArg3' with the active site of thrombin were essentially identical to those of related structures of PPACK- (D-Phe-Pro-Arg chloromethyl ketone) and hirulog 1-thrombin, with the guanidinium function of the arginyl P1 residue forming a hydrogen-bonding ion pair with Asp189 of the S1 site. A noticeable shift in the CA atom of beta-homoArg3' due to the methylene insertion displaces the scissile bond from attack by Ser195, thus imparting proteolytic stability to the beta-homoArg hirulog derivative. Resolution of the pentaglycine spacer, linking N- and C-terminal functional domains into a single oligopeptide bivalent inhibitor, permitted delineation of corresponding S' subsites of thrombin. The position of Gly4' (P1') is stabilized by three hydrogen bonds with His57, Lys60F, and Ser195, while the conformational angles maintained in a strained, nonallowed configuration for non-glycyl amino acids.(ABSTRACT TRUNCATED AT 250 WORDS)

Dynamic bandwidth allocation in a network

Recently protocols have been introduced which enable us to integrate periodic traffic (voice or video) and aperiodic traffic (data) and to extend the size of local area networks without any loss in speed and capacity. One of these, the DRAMA protocol, is based on broadband technology and allows for dynamic allocation of bandwidth to clusters of nodes in the total network. In this paper we propose a distributed algorithm to allocate bandwidth in a fair manner, where we have defined fair to mean that every node in the network, regardless of its location, should have the same expected access delay to the net. We show by means of simulation that the algorithm is stable and within a few percentage points of the optimal solution. Stability is measured in terms of the time it takes the system to return to near optimal distribution of the bandwidth after strong disturbances. The algorithm is shown to handle total reallocation of the resources within O(100ms).