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PubMed2005

The two major oligomeric forms of human mannan-binding lectin: chemical characterization, carbohydrate-binding properties, and interaction with MBL-associated serine proteases.

Mannan-binding lectin (MBL) is an oligomeric C-type lectin assembled from homotrimeric structural units that binds to neutral carbohydrates on microbial surfaces. It forms individual complexes with MBL-associated serine proteases (MASP)-1, -2, -3 and a truncated form of MASP-2 (MAp19) and triggers the lectin pathway of complement through MASP-2 activation. To characterize the oligomerization state of the two major MBL forms present in human serum, both proteins were analyzed by mass spectrometry. Mass values of 228,098 +/- 170 Da (MBL-I) and 304,899 +/- 229 Da (MBL-II) were determined for the native proteins, whereas reduction of both species yielded a single chain with an average mass of 25,340 +/- 18 Da. This demonstrates that MBL-I and -II contain 9 and 12 disulfide-linked chains, respectively, and therefore are trimers and tetramers of the structural unit. As shown by surface plasmon resonance spectroscopy, trimeric and tetrameric MBL bound to immobilized mannose-BSA and N-acetylglucosamine-BSA with comparable K(D) values (2.2 and 0.55 nM and 1.2 and 0.96 nM, respectively). However, tetrameric MBL exhibited significantly higher maximal binding capacity and lower dissociation rate constants for both carbohydrates. In contrast, no significant difference was detected for binding of the recombinant MASPs or MAp19 to immobilized trimeric or tetrameric MBL. As shown by gel filtration, both MBL species formed 1:2 complexes with MASP-3 or MAp19. These results provide the first precise analysis of the major human MBL oligomers. The oligomerization state of MBL has a direct effect on its carbohydrate-binding properties, but no influence on the interaction with the MASPs.

Acetylglucosamine↗
PubMed1996

Trimeric interactions of the invariant chain and its association with major histocompatibility complex class II alpha beta dimers.

The invariant chain (I chain) associates with major histocompatibility complex class II alphabeta heterodimers upon synthesis, preventing them from binding peptides and unfolded proteins in the endoplasmic reticulum and directing class II transport to post-Golgi endosomal compartments. To assess which regions of the I chain are involved in binding class II molecules, we have studied proteolytic fragments of the I chain generated both by natural proteolytic degradation of alphabeta dimer-invariant chain complexes (alphabeta.I) within human B cells and by in vitro digestion of purified alphabeta middle dotI complexes with proteinase K. The 18-kDa luminal I chain fragment generated by proteinase K, called K3, remains associated with alphabeta dimers and retains the complex (alphabeta.K3) in a high molecular mass nonameric configuration. The N terminus of the K3 fragment was identified as glycine 110. This indicates that the K3 fragment lies outside of the class II-associated invariant chain peptide region (amino acids 81-104) of the I chain, shown to be important for initial alphabeta.I assembly. An N-terminal 12-kDa I chain fragment called p12, generated intracellularly, was also analyzed and was found to remain associated with alphabeta dimers in a high molecular mass form analogous to the nonameric alphabeta.I complex. These results demonstrate that at least two class II contact points exist along the length of the I chain and that different regions of the I chain can stabilize the alphabeta.I nonamer. Additional evidence suggests that the O-linked glycan(s) characteristic of the I chain is added to the short C-terminal region absent from the K3 fragment.

Antigens, Differentiation, B-Lymphocyte↗
PubMed2001

Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction.

The crystal structure of a novel Cre-Lox synapse was solved using phases from multiple isomorphous replacement and anomalous scattering, and refined to 2.05 A resolution. In this complex, a symmetric protein trimer is bound to a Y-shaped three-way DNA junction, a marked departure from the pseudo-4-fold symmetrical tetramer associated with Cre-mediated LoxP recombination. The three-way DNA junction was accommodated by a simple kink without significant distortion of the adjoining DNA duplexes. Although the mean angle between DNA arms in the Y and X structures was similar, adjacent Cre trimer subunits rotated 29 degrees relative to those in the tetramers. This rotation was accommodated at the protein-protein and DNA-DNA interfaces by interactions that are "quasi-equivalent" to those in the tetramer, analogous to packing differences of chemically identical viral subunits at non-equivalent positions in icosahedral capsids. This structural quasi-equivalence extends to function as Cre can bind to, cleave and perform strand transfer with a three-way Lox substrate. The structure explains the dual recognition of three and four-way junctions by site-specific recombinases as being due to shared structural features between the differently branched substrates and plasticity of the protein-protein interfaces. To our knowledge, this is the first direct demonstration of quasi-equivalence in both the assembly and function of an oligomeric enzyme.

Attachment Sites, Microbiological↗
PubMed1994

Aluminum fluoride acts on the reversibility of ARF1-dependent coat protein binding to Golgi membranes.

The GTP-dependent interaction of ADP ribosylation factor 1 (ARF1) with Golgi membranes is required for the binding of cytosolic coatomer proteins to those membranes. Whereas both GTP and GTP gamma S can support coatomer binding to membranes, by using partially purified components, GTP-driven binding is rapidly reversible (t1/2 of 2 min) while that driven by GTP gamma S is more stable (t1/2 of over 30 min). In the presence of GTP, aluminum fluoride, an activator of trimeric G proteins, promotes the stable ARF-dependent binding of coatomer to membranes, even though this reagent does not itself activate ARF. Aluminum fluoride appears to act, like GTP gamma S, to make the binding of coatomer relatively irreversible. It acts to inhibit ARF-GTP hydrolysis catalyzed by the membrane and thus makes the ARF-GTP active state persistent. This effect is not dependent on the presence of any cytosolic component, such as the coatomer. The number of molecules of ARF that can be protected from hydrolysis by aluminum fluoride, however, is only a fraction of the total amount of ARF that can bind to membranes in the presence of GTP gamma S. We propose that this population defines a set of binding sites that are sufficient for coat protein assembly onto the membrane.

ADP-Ribosylation Factor 1↗
PubMed2005

The structure of the human adenovirus 2 penton.

The adenovirus penton, a noncovalent complex of the pentameric penton base and trimeric fiber proteins, comprises the vertices of the adenovirus capsid and contains all necessary components for viral attachment and internalization. The 3.3 A resolution crystal structure of human adenovirus 2 (hAd2) penton base shows that the monomer has a basal jellyroll domain and a distal irregular domain formed by two long insertions, a similar topology to the adenovirus hexon. The Arg-Gly-Asp (RGD) motif, required for interactions with cellular integrins, occurs on a flexible surface loop. The complex of penton base with bound N-terminal fiber peptide, determined at 3.5 A resolution, shows that the universal fiber motif FNPVYPY binds at the interface of adjacent penton base monomers and results in a localized structural rearrangement in the insertion domain of the penton base. These results give insight into the structure and assembly of the adenovirus capsid and will be of use for gene-therapy applications.

Adenoviruses, Human↗
PubMed1995

The role of coiled-coil alpha-helices and disulfide bonds in the assembly and stabilization of cartilage matrix protein subunits. A mutational analysis.

Cartilage matrix protein (CMP) exists as a disulfide-bonded homotrimer in the matrix of cartilage. Each monomer consists of two CMP-A domains that are separated by an epidermal growth factor-like domain. A heptad repeat-containing tail makes up the carboxyl-terminal domain of the protein. The secreted form of CMP contains 12 cysteine residues numbered C1 through C12. Two of these are in each of the CMP-A domains, six are in the epidermal growth factor-like domain, and two are in the heptad repeat-containing tail. Two major categories of mutant CMPs were generated to analyze the oligomerization process of CMP: a mini-CMP and a heptadless full-length CMP. The mini-CMP consists of the CMP-A2 domain and the heptad repeat-containing tail. In addition, a number of mutations affecting C9 through C12 were generated within the full-length, the mini-, and the heptad-less CMPs. The mutational analysis indicates that the heptad repeats are necessary for the initiation of CMP trimerization and that the two cysteines in the heptad repeat-containing tail are both necessary and sufficient to form intermolecular disulfide bonds in either full-length or mini-CMP. The two cysteines within a CMP-A domain form an intradomain disulfide bond.

Amino Acid Sequence↗
PubMed2000

The central proline of an internal viral fusion peptide serves two important roles.

The fusion peptide of the avian sarcoma/leukosis virus (ASLV) envelope protein (Env) is internal, near the N terminus of its transmembrane (TM) subunit. As for most internal viral fusion peptides, there is a proline near the center of this sequence. Robson-Garnier structure predictions of the ASLV fusion peptide and immediate surrounding sequences indicate a region of order (beta-sheet), a tight reverse turn containing the proline, and a second region of order (alpha-helix). Similar motifs (order, turn or loop, order) are predicted for other internal fusion peptides. In this study, we made and analyzed 12 Env proteins with substitutions for the central proline of the fusion peptide. Env proteins were expressed in 293T cells and in murine leukemia virus pseudotyped virions. We found the following. (i) All mutant Envs form trimers, but when the bulky hydrophobic residues phenylalanine or leucine are substituted for proline, trimerization is weakened. (ii) Surprisingly, the proline is required for maximal processing of the Env precursor into its surface and TM subunits; the amount of processing correlates linearly with the propensity of the substituted residue to be found in a reverse turn. (iii) Nonetheless, proteolytically processed forms of all Envs are preferentially incorporated into pseudotyped virions. (iv) All Envs bind receptor with affinity greater than or equal to wild-type affinity. (v) Residues that support high infectivity cluster with proline at intermediate hydrophobicity. Infectivity is not supported by mutant Envs in which charged residues are substituted for proline, nor is it supported by the trimerization-defective phenylalanine and leucine mutants. Our findings suggest that the central proline in the ASLV fusion peptide is important for the formation of the native (metastable) Env structure as well as for membrane interactions that lead to fusion.

Alpharetrovirus↗
PubMed2002

Design and structural extension of a supramolecular inclusion-compound host made by the formation of dimers of isonicotinic acid and thiocyanato coordinating bridges.

A new host design for an inclusion compound with a preference for large planar aromatic guest molecules has been proposed. Our host design includes a rectangular cavity made using a long and a short building block based on the concept of supramolecular chemistry. The long building block facilitates the inclusion of large guests, and the short building block prevents the formation of an interpenetrated structure, which is often observed in frameworks with large void spaces. The long building block is made when dimers of 4-pyridinecarboxylic acid (isoH) form through hydrogen bonding between the two carboxylic acid moieties. This isoH dimer can link two transition metal centers using the N atoms at both ends to act as a long building block. For the short building block, the thiocyanato ion was used. This makes a bent bridge between two metal centers to form a 1D double-chain [M(SCN)2]infinity complex. From the self-assembly of isoH, SCN- and Ni2+, a 2D network of [Ni(SCN)2(isoH)2]infinity, in which the 1D [Ni(SCN)2]infinity complexes are linked by the isoH dimers, is built up. The rectangular cavity is formed as a mesh within the 2D network. The crystal of our inclusion compound has a layered structure of 2D networks, and a 1D channel-like cavity penetrating the layered 2D networks is formed where guests may be included. Moreover, our host design has the advantage of easy extension of the host structure. Replacement of isoH with another component and use of three components is possible for making the long building block. In the latter case, a linear spacer having two carboxy groups is inserted into the isoH dimer to form a long building block with a trimer structure. Based on our host design, a series of new inclusion compounds were synthesized. The crystal structures of three compounds were determined by single crystal X-ray diffraction. These were a biphenyl inclusion compound [Ni(SCN)2(isoH)2].1/2C12H10 (the basic case), a 9,10-dichloroanthracene inclusion compound [Ni(SCN)2(acrylH)2].1/2C14H8Cl2, where isoH is replaced with 3-(4-pyridinyl)-2-propenoic acid (acrylH), and a perylene inclusion compound [Ni(SCN)2(isoH)2(fumaricH2)].1/2C20H12, whose long building block is a trimer inserted with fumaric acid (fumaricH2) as a linear spacer.

Journal Article↗
PubMed2002

First preparation of spacer-linked cyclic neooligoaminodeoxysaccharides.

The preparation of novel cyclic 1,4-butanediol-linked oligoaminodeoxysugars 3-5 and 7 is described which are potential binders to polynucleotides. Neooligosaccharides 3-5 are assembled by two consecutive metathesis protocols. In the first phase metathesis-mediated dimerization of an aminodeoxymonosaccharide which was either allylated at the anomeric center or at C4 led to E/Z mixtures of C2-symmetric homodimers which were transformed into the corresponding 1,4-butanediol linked disaccharides by catalytic hydrogenation of the central olefinic double bond. Double Q-allylation of the head-to-head dimer set the stage for macrocyclization by means of ring-closing metathesis. This ring-closing process was highly dependent of the configuration in the carbohydrate moieties. arabino-Configured homodimer 15 directly yielded the macrocycle 32 which contains two sugar units while under the same metathesis conditions the corresponding ribo-configured starting homodimer 19 afforded cyclic neotetra- and neohexasaccharides 34 and 35 after a preceding dimerization and trimerization step, respectively. In addition, homodimer 23 was coupled with silylglycoside 14a under Lewis-acid promoted glycosidation conditions to furnish the doubly glycosylated homodimer 31. Ring-closing metathesis afforded the macrocyclic neoaminodeoxyoligosaccharide 36 with alternating 1,4-butanediol linkage and glycosidic bond. The primary cyclization products were finally transformed into the respective cyclic neoaminodeoxyoligosaccharides 3-5 and 7 by catalytic hydrogenation and standard deprotection conditions.

Amino Sugars↗
PubMed2001

Converting a DNA damage checkpoint effector (UmuD2C) into a lesion bypass polymerase (UmuD'2C).

During the SOS response of Escherichia coli to DNA damage, the umuDC operon is induced, producing the trimeric protein complexes UmuD2C, a DNA damage checkpoint effector, and UmuD'2C (DNA polymerase V), which carries out translesion synthesis, the basis of 'SOS mutagenesis'. UmuD'2, the homodimeric component of DNA pol V, is produced from UmuD by RecA-facilitated self-cleavage, which removes the 24 N-terminal residues of UmuD. We report the solution structure of UmuD'2 (PDB ID 1I4V) and interactions within UmuD'-UmuD, a heterodimer inactive in translesion synthesis. The overall shape of UmuD'2 in solution differs substantially from the previously reported crystal structure, even though the topologies of the two structures are quite similar. Most significantly, the active site residues S60 and K97 do not point directly at one another in solution as they do in the crystal, suggesting that self-cleavage of UmuD might require RecA to assemble the active site. Structural differences between UmuD'2 and UmuD'- UmuD suggest that UmuD'2C and UmuD2C might achieve their different biological activities through distinct interactions with RecA and DNA pol III.

Amino Acid Sequence↗
PubMed1997

Membrane binding of human immunodeficiency virus type 1 matrix protein in vivo supports a conformational myristyl switch mechanism.

The interaction of the human immunodeficiency virus (HIV) Gag protein with the plasma membrane of a cell is a critical event in the assembly of HIV particles. The matrix protein region (MA) of HIV type 1 (HIV-1) Pr55Gag has previously been demonstrated to confer membrane-binding properties on the precursor polyprotein. Both the myristic acid moiety and additional determinants within MA are essential for plasma membrane binding and subsequent particle formation. In this study, we demonstrated the myristylation-dependent membrane interaction of MA in an in vivo membrane-binding assay. When expressed within mammalian cells, MA was found both in association with cellular membranes and in a membrane-free form. In contrast, the intact precursor Pr55Gag molecule analyzed in an identical manner was found almost exclusively bound to membranes. Both membrane-bound and membrane-free forms of MA were myristylated and phosphorylated. Differential membrane binding was not due to the formation of multimers, as dimeric and trimeric forms of MA were also found in both membrane-bound and membrane-free fractions. To define the requirements for membrane binding of MA, we analyzed the membrane binding of a series of MA deletion mutants. Surprisingly, deletions within alpha-helical regions forming the globular head of MA led to a dramatic increase in overall membrane binding. The stability of the MA-membrane interaction was not affected by these deletions, and no deletion eliminated membrane binding of the molecule. These results establish that myristic acid is a primary determinant of the stability of the Gag protein-membrane interaction and provide support for the hypothesis that a significant proportion of HIV-1 MA molecules may adopt a conformation in which myristic acid is hidden and unavailable for membrane interaction.

Animals↗
PubMed2004

Protective immunoglobulin A and G antibodies bind to overlapping intersubunit epitopes in the head domain of type 1 reovirus adhesin sigma1.

Nonfusogenic mammalian orthoreovirus (reovirus) is an enteric pathogen of mice and a useful model for studies of how an enteric virus crosses the mucosal barrier of its host and is subject to control by the mucosal immune system. We recently generated and characterized a new murine immunoglobulin A (IgA)-class monoclonal antibody (MAb), 1E1, that binds to the adhesin fiber, sigma1, of reovirus type 1 Lang (T1L) and thereby neutralizes the infectivity of that strain in cell culture. 1E1 is produced in hybridoma cultures as a mixture of monomers, dimers, and higher polymers and is protective against peroral challenges with T1L either when the MAb is passively administered or when it is secreted into the intestines of mice bearing subcutaneous hybridoma tumors. In the present study, selection and analysis of mutants resistant to neutralization by 1E1 identified the region of T1L sigma1 to which the MAb binds. The region bound by a previously characterized type 1 sigma1-specific neutralizing IgG MAb, 5C6, was identified in the same way. Each of the 15 mutants isolated and analyzed was found to be much less sensitive to neutralization by either 1E1 or 5C6, suggesting the two MAbs bind to largely overlapping regions of sigma1. The tested mutants retained the capacity to recognize specific glycoconjugate receptors on rabbit M cells and cultured epithelial cells, even though viral binding to epithelial cells was inhibited by both MAbs. S1 sequence determinations for 12 of the mutants identified sigma1 mutations at four positions between residues 415 and 447, which contribute to forming the receptor-binding head domain. When aligned with the sigma1 sequence of reovirus type 3 Dearing (T3D) and mapped onto the previously reported crystal structure of the T3D sigma1 trimer, the four positions cluster on the side of the sigma1 head, across the interface between two subunits. Three such interface-spanning epitopes are thus present per sigma1 trimer and require the intact quaternary structure of the head domain for MAb binding. Identification of these intersubunit epitopes on sigma1 opens the way for further studies of the mechanisms of antibody-based neutralization and protection with type 1 reoviruses.

Amino Acid Substitution↗
PubMed1991

Calcium-dependent complex assembly of the myeloic differentiation proteins MRP-8 and MRP-14.

MRP-8 and MRP-14 are calcium-binding proteins belonging to the S-100 protein family which have been shown to be associated with specific stages of myeloic/monocytic cell differentiation. Members of this protein family are shown to form homo- and heterodimers. Complex formation has also been observed in preliminary experiments for MRP-8 and MRP-14. To evaluate the in vivo relevance of the MRP complex formation and the stoichiometric ratio of individual components complexes were isolated from granulocytes and monocytes by immunoaffinity chromatography using monospecific antibodies. The purified fraction of the MRPs was found to contain monomers and dimers as shown on sodium dodecyl sulfate-polyacrylamide gel electrophoresis by silver staining and immunoblotting. Similar results were obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting of crude cell extracts. The existence of the MRP complexes in vivo was demonstrated by chemical cross-linking and subsequent isolation of complexes by immunoaffinity chromatography. Two new, highly abundant complexes were found in addition to the heterodimer, but neither monomers nor homodimers were detected. The two larger protein complexes (35.0 and 48.5 kDa) were identified as [MRP-8)2.(MRP-14] trimer and [MRP-8)2.(MRP-14)2) tetramer, respectively. All complexes could be shown to be noncovalently associated in vivo. Furthermore, the association of MRPs was shown to be Ca2+ dependent.

Blotting, Western↗
PubMed2005

Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis.

The structural and mechanical properties of monomeric actin (G-actin), the trimer nucleus, and actin filaments (F-actins) are determined as a function of the conformation of the DNase I-binding loop (DB loop) by using all-atom molecular dynamics simulations and coarse-grained (CG) analysis. Recent x-ray structures of ADP-bound G-actin (G-ADP) by Otterbein et al. [Otterbein, L. R., Graceffa, P. & Dominguez, R. (2001) Science 293, 708-711] and ATP-bound G-actin (G-ATP) by Graceffa and Dominguez [Graceffa, P. & Dominguez, R. (2003) J. Biol. Chem. 278, 34172-34180] indicate that the DB loop of actin does not have a well defined secondary structure in the ATP state but folds into an alpha-helix in the ADP state. MD simulations and CG analysis indicate that such a helical DB loop significantly weakens the intermonomer interactions of actin assemblies and thus leads to a wider, shorter, and more disordered filament. The computed persistence lengths of F-actin composed of G-ATP (16 microm) and of G-ADP (8.5 microm) agree well with the experimental values for the two states. Therefore, the loop-to-helix transition of the DB loop may be one of the factors that lead to the changes in structural and mechanical properties of F-actin after ATP hydrolysis. This result may provide a direct connection between the conformational changes of an actin monomer and the structural and mechanical properties of the cytoskeleton. The information provided by MD simulations also helps to understand the possible origin of the special features of actin dynamics.

Actin Cytoskeleton↗
PubMed1996

Triple helix formation of procollagen type I can occur at the rough endoplasmic reticulum membrane.

One key problem in understanding the biosynthesis of collagens remains the assembly of the three alpha-chains. How and when are the different gene products selected, aligned, and folded into a triple helix? As the spatial arrangement during biosynthesis might be important, we concentrated on whether the rough endoplasmic reticular membrane is involved in this process. Microsomes were prepared from biosynthetically labeled chick tendon fibroblasts. Vesicles were spread as a monomolecular film which was then transferred over several compartments of a filmbalance containing fresh subphase. Fluorograms of the surface film showed that the monolayer contains procollagen chains. When the monolayer was transferred onto a chymotrypsin/trypsin-containing subphase, the gel bands of the proalpha-chains were shifted into the position of mature alpha-chains, indicating that only the propeptides were digested and the collagenous regions were protected due to triple helix formation. Our results suggest that newly synthesized proalpha-chains can associate as trimers and fold into a triple helical conformation while they are still associated with the membranes of the rough endoplasmic reticulum. These processes also occur when interchain disulfide linkage is inhibited, indicating that chain selection and registration is not dependent on formation of covalent bonds among the carboxyl propeptides.

Animals↗
PubMed1998

A novel three-dimensional crystal of bacteriorhodopsin obtained by successive fusion of the vesicular assemblies.

When the two-dimensional crystal of bacteriorhodopsin (bR), purple membrane, is incubated at high temperature (32 degreesC) with a small amount of the neutral detergent octylthioglucoside in the presence of the precipitant ammonium sulfate, a large fraction of the membrane fragments is converted into spherical vesicles with a diameter of 50 nm, which are able to assemble into optically isotropic hexagonal crystals when the precipitant concentration is increased. The vesicularization of purple membrane takes place under such a condition that the miscibility of the detergent to the aqueous phase becomes very low, and we suggest that it is initiated by insertion of the detergent molecules into the membrane. At low temperature, the transformation into the vesicular structure is inhibited and no large crystal is produced directly from membrane/detergent/precipitant mixtures. When a suspension of the spherical vesicles produced at the high temperature is cooled and concentrated below 15 degreesC, however, a birefringent hexagonal crystal is produced that diffracts X-rays beyond 2.5 A resolution. This new crystal belongs to the space group P622 with unit cell dimensions of a=b=104.7 A and c=114.1 A, and it is shown to be made up of stacked planar membranes, in each of which the bR trimers are arranged on a honeycomb lattice and the space among the proteins is filled with the detergent molecules and native lipids. These stacked membranes are suggested to be produced by successive fusion of the spherical vesicles. This implies that the crystallization is achieved without any step for complete solubilization of the protein. The present result offers a unique crystallization method that may be applicable to such membrane proteins that are liable to denature in the presence of an excess amount of detergent.

Bacteriorhodopsins↗
PubMed2006

Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus.

A new method for predicting interacting residues in protein complexes, InterProSurf, was applied to the E1 envelope protein of Venezuelan equine encephalitis (VEEV). Monomeric and trimeric models of VEEV-E1 were constructed with our MPACK program, using the crystal structure of the E1 protein of Semliki forest virus as a template. An alignment of the E1 sequences from representative alphavirus sequences was used to determine physical chemical property motifs (likely functional areas) with our PCPMer program. Information on residue variability, propensity to be in protein interfaces, and surface exposure on the model was combined to predict surface clusters likely to interact with other viral or cellular proteins. Mutagenesis of these clusters indicated that the predictions accurately detected areas crucial for virus infection. In addition to the fusion peptide area in domain 2, at least two other surface areas play an important role in virus infection. We propose that these may be sites of interaction between the E1-E1 and E1-E2 subdomains of the envelope proteins that are required to assemble the functional unit. The InterProSurf method is, thus, an important new tool for predicting viral protein interactions. These results can aid in the design of new vaccines against alphaviruses and other viruses.

Amino Acids↗
PubMed2001

The structure and biological features of fibrinogen and fibrin.

Fibrinogen and fibrin play important, overlapping roles in blood clotting, fibrinolysis, cellular and matrix interactions, inflammation, wound healing, and neoplasia. These events are regulated to a large extent by fibrin formation itself and by complementary interactions between specific binding sites on fibrin(ogen) and extrinsic molecules including proenzymes, clotting factors, enzyme inhibitors, and cell receptors. Fibrinogen is comprised of two sets of three polypeptide chains termed A alpha, B beta, and gamma, that are joined by disulfide bridging within the N-terminal E domain. The molecules are elongated 45-nm structures consisting of two outer D domains, each connected to a central E domain by a coiled-coil segment. These domains contain constitutive binding sites that participate in fibrinogen conversion to fibrin, fibrin assembly, crosslinking, and platelet interactions (e.g., thrombin substrate, Da, Db, gamma XL, D:D, alpha C, gamma A chain platelet receptor) as well as sites that are available after fibrinopeptide cleavage (e.g., E domain low affinity non-substrate thrombin binding site); or that become exposed as a consequence of the polymerization process (e.g., tPA-dependent plasminogen activation). A constitutive plasma factor XIII binding site and a high affinity non-substrate thrombin binding site are located on variant gamma' chains that comprise a minor proportion of the gamma chain population. Initiation of fibrin assembly by thrombin-mediated cleavage of fibrinopeptide A from A alpha chains exposes two EA polymerization sites, and subsequent fibrinopeptide B cleavage exposes two EB polymerization sites that can also interact with platelets, fibroblasts, and endothelial cells. Fibrin generation leads to end-to-middle intermolecular Da to EA associations, resulting in linear double-stranded fibrils and equilaterally branched trimolecular fibril junctions. Side-to-side fibril convergence results in bilateral network branches and multistranded thick fiber cables. Concomitantly, factor XIII or thrombin-activated factor XIIIa introduce intermolecular covalent epsilon-(gamma glutamyl)lysine bonds into these polymers, first creating gamma dimers between properly aligned C-terminal gamma XL sites, which are positioned transversely between the two strands of each fibrin fibril. Later, crosslinks form mainly between complementary sites on alpha chains (forming alpha-polymers), and even more slowly among gamma dimers to create higher order crosslinked gamma trimers and tetramers, to complete the mature network structure.

Binding Sites↗