Structures of thrombin complexes with a designed and a natural exosite peptide inhibitor

The structures of two hirudin-based fibrinogen recognition exosite peptide inhibitors with significantly different sequences complexed with alpha-thrombin at a site distinct from the active site (exosite) have been determined crystallographically at 2.2 and 2.3 A resolution. One is a designed synthetic peptide with some nonconventional amino acid residues (MDL-28050), and the other is a natural COOH-terminal peptide isolated from the leech Hirudinaria manillensis (hirullin P18). The structures have been refined by restrained least squares methods to R values of 0.161 and 0.155, respectively. The first stretch of each peptide, corresponding to hirudin 55-59, associates with thrombin similar to hirudin and hirugen (hirudin 53-64). Although the remaining residues of the inhibitors interact with and bind to thrombin, the binding is accomplished. through a rigid body conformational adjustment of the peptide with respect to the conformation displayed by hirudin and hirugen (40 degrees rotation about the Ile59, CA-C bond). This causes the side groups of cyclohexylalanine 64' of MDL-28050 and Ile60, of hirullin to point in the opposite direction of the all important Tyr63, ring of hirudin and hirugen but permits the residues to penetrate and interact with the 3(10) turn hydrophobic binding pocket of thrombin. Thus, the hydrophobic interaction is accomplished in a different way by virtue of the substrate conformational readjustment. The results show that the first stretch of peptide makes concerted and efficient binding interactions with thrombin, and the peptide positions of the inhibitors are fairly specific and homologous so that the stretch appears to be related to specific recognition associated with the exosite. The relative flexibility of structure and sequence of the second stretch is a display of tolerance of imprecision by thrombin in its COOH-terminal hydrophobic association with hirudin-based inhibitors.

Molecular basis for the inhibition of human alpha-thrombin by the macrocyclic peptide cyclotheonamide A

The macrocyclic peptide cyclotheonamide A (CtA), isolated from the marine sponge Theonella sp., represents an unusual class of serine protease inhibitor. A complex of this inhibitor with human alpha-thrombin, a protease central to the bioregulation of thrombosis and hemostasis, was studied by x-ray crystallography. This work (2.3-A resolution) confirms the structure of CtA and reveals intimate details about its molecular recognition within the enzyme active site. Interactions due to the "Pro-Arg motif" (Arg occupancy of the S1 specificity pocket; formation of a hydrogen-bonded two-strand antiparallel beta-sheet with Ser214-Gly216) and the alpha-keto amide group of CtA are primarily responsible for binding to thrombin, with the alpha-keto amide serving as a transition-state analogue. A special interaction with the "insertion loop" of thrombin (Tyr60A-Thr60I) is manifested through engagement of the hydroxyphenyl group of CtA with Trp60D as part of an "aromatic stacking chain." Biochemical inhibition data (Ki values at 37 degrees C) were obtained for CtA with thrombin and a diverse collection of serine proteases. Thus, CtA is just a moderate inhibitor of human alpha-thrombin (Ki = 0.18 microM) but a potent inhibitor of trypsin (Ki = 0.023 microM) and streptokinase (Ki = 0.035 microM). The relative lack of potency of CtA as a thrombin inhibitor is discussed with respect to certain structural features of the enzyme complex. We also report the total synthesis of CtA, by a convergent [2 + 3] fragment-condensation approach, to serve the preparation of cyclotheonamide analogues for structure-function studies.

Magnetically induced orientation of phosphatidylcholine membranes

Lipid bilayers prepared from natural phospholipids orient in magnetic fields with the long axis of the lipid molecules perpendicular to the magnetic field. This magnetically induced orientation was studied at high (11.7 Tesla (T)), mid (9.36 T), and low (4.68 T) magnetic field strengths using lipid aggregates prepared from natural and synthetic phosphatidylcholine analogs. Phosphatidylcholine analogs containing saturated diacylated chains (12 to 16 carbons/chain) exhibited extensive orientation of the lipid when bilayer formation occurred by gentle hydration conditions. Gentle hydration involved incubating dried phosphatidylcholine C above the main phase transition (Tm); brief shaking or swirling by hand was occasionally needed to completely disperse the lipids. The method of bilayer formation significantly influenced the amount of lipid that orients in magnetic fields. Thus the supramolecular structures (and % orientation) above Tm in an 11.7 T field of dimyristoylphosphatidylcholine (DMPC) bilayers are SUV (0%), LUV (approximately 15%), SPLV (approximately 40%), vortexed-MLV (approximately 60%) and non-vortexed MLV (approximately 90%). Single layered vesicles prepared by the REV method exhibited orientation at 11.7 T similar to LUV prepared by freeze thaw cycles. Aqueous dispersions of eggPC prepared by gentle hydration exhibit approximately 40% orientation at 11.7 T which decreased to approximately 30% orientation if 30% cholesterol is added to the membrane. Magnetic orientation of bilayers thus appears to be a general phenomenon for both saturated and unsaturated natural phospholipids either with or without cholesterol in the membrane.

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).