Divi Venkateswarlu

Structure and Dynamics of Zymogen Human Blood Coagulation Factor X

The solution structure and dynamics of the human coagulation factor X (FX) have been investigated to understand the key structural elements in the zymogenic form that participates in the activation process. The model was constructed based on the 2.3-A-resolution x-ray crystallographic structure of active-site inhibited human FXa (PDB:1XKA). The missing gamma-carboxyglutamic acid (GLA) and part of epidermal growth factor 1 (EGF1) domains of the light chain were modeled based on the template of GLA-EGF1 domains of the tissue factor (TF)-bound FVIIa structure (PDB:1DAN). The activation peptide and other missing segments of FX were introduced using homology modeling. The full calcium-bound model of FX was subjected to 6.2 ns of molecular dynamics simulation in aqueous medium using the AMBER6.0 package. We observed significant reorientation of the serine-protease (SP) domain upon activation leading to a compact multi-domain structure. The solution structure of zymogen appears to be in a well-extended conformation with the distance between the calcium ions in the GLA domain and the catalytic residues estimated to be approximately 95 A in contrast to approximately 83 A in the activated form. The latter is in close agreement with fluorescence studies on FXa. The S1-specificity residues near the catalytic triad show significant differences between the zymogen and activated structures.

TAUTOMERIC EQUILIBRIA IN 8-OXOPURINES: IMPLICATIONS FOR MUTAGENICITY

Free-radical-induced DNA damage by ionizing radiation leads to a number of oxidized purines, of which 7H-8-oxoguanine (8OG) and 7H-8-oxoadenine (8OA) are predominant and known to cause an appreciable amount of cellular damage. A detailed quantum mechanical study at various levels of theory in both the gas phase and in an aqueous solution has been carried out in order to assess the tautomeric preferences of the bases. The calculated energies of various plausible tautomers suggest that at higher levels of ab initio theory with inclusion of electron correlation, the 8-keto-6-enolic form of 8-oxoguanine (8OG2) would predominate over the 6,8-diketo form (8OG1) in the gas phase whereas the 6-amino-8-keto form (8OA1) predominates over the other possible tautomers of 8-oxoadenine. Aqueous solvation, however, changes the gas-phase order for 8-oxoguanine, 8OG1 turning out to be the major tautomeric species in an aqueous medium. The estimated free energies of hydration by polarized continuum models are indicative that the mutagenically significant amounts of minor tautomeric forms of 8-oxoguanine and 8-oxoadenine exist in the aqueous phase and might be held responsible for inducing transversional as well as transitional mutations.

An all‐atom solution‐equilibrated model for human extrinsic blood coagulation complex (sTF–VIIa–Xa): a protein–protein docking and molecular dynamics refinement study

Summary.  Tissue factor (TF)‐bound factor (F)VIIa plays a critical role in activating FX, an event that rapidly results in blood coagulation. Despite recent advances in the structural information about soluble TF (sTF)‐bound VIIa and Xa individually, the atomic details of the ternary complex are not known. As part of our long‐term goal to provide a structural understanding of the extrinsic blood coagulation pathway, we built an all atom solution‐equilibrated model of the human sTF–VIIa–Xa ternary complex using protein–protein docking and molecular dynamics (MD) simulations. The starting structural coordinates of sTF–VIIa and Xa were derived from dynamically equilibrated solution structures. Due to the flexible nature of the light‐chain of the Xa molecule, a three‐stage docking approach was employed in which SP (Arg195‐Lys448)/EGF2 (Arg86‐Arg139), EGF1 (Asp46‐Thr85) and GLA (Ala1‐Lys45) domains were docked in a sequential manner. The rigid‐body docking approach of the FTDOCK method in conjunction with filtering based on biochemical knowledge from experimental site‐specific mutagenesis studies provided the strategy. The best complex obtained from the docking experiments was further refined using MD simulations for 3 ns in explicit water. In addition to explaining most of the known experimental site‐specific mutagenesis data pertaining to sTF–VIIa, our model also characterizes likely enzyme‐binding exosites on FVIIa and Xa that may be involved in the ternary complex formation. According to the equilibrated model, the 140s loop of VIIa serves as the key recognition motif for complex formation. Stable interactions occur between the FVIIa 140s loop and the FXa β‐strand B2 region near the sodium‐binding domain, the 160 s loop and the N‐terminal activation loop regions. The helical‐hydrophobic stack region that connects the GLA and EGF1 domains of VIIa and Xa appears to play a potential role in the membrane binding region of the ternary complex. The proposed model may serve as a reasonable structural basis for understanding the exosite‐mediated substrate recognition of sTF–VIIa and to advance understanding of the TFPI‐mediated regulatory pathway of the extrinsic blood coagulation cascade.

Structural investigation of zymogenic and activated forms of human blood coagulation factor VIII: a computational molecular dynamics study.

BackgroundHuman blood coagulation factor VIII (fVIII) is a large plasma glycoprotein with sequential domain arrangement in the order A1-a1-A2-a2-B-a3-A3-C1-C2. The A1, A2 and A3 domains are interconnected by long linker peptides (a1, a2 and a3) that possess the activation sites. Proteolysis of fVIII zymogen by thrombin or factor Xa results in the generation of the activated form (fVIIIa) which serves as a critical co-factor for factor IXa (fIXa) enzyme in the intrinsic coagulation pathway.ResultsIn our efforts to elucidate the structural differences between fVIII and fVIIIa, we developed the solution structural models of both forms, starting from an incomplete 3.7 Å X-ray crystal structure of fVIII zymogen, using explicit solvent MD simulations. The full assembly of B-domainless single-chain fVIII was built between the A1-A2 (Ala1-Arg740) and A3-C1-C2 (Ser1669-Tyr2332) domains. The structural dynamics of fVIII and fVIIIa, simulated for over 70 ns of time scale, enabled us to evaluate the integral motions of the multi-domain assembly of the co-factor and the possible coordination pattern of the functionally important calcium and copper ion binding in the protein.ConclusionsMD simulations predicted that the acidic linker peptide (a1) between the A1 and A2 domains is largely flexible and appears to mask the exposure of putative fIXa enzyme binding loop (Tyr555-Asp569) region in the A2 domain. The simulation of fVIIIa, generated from the zymogen structure, predicted that the linker peptide (a1) undergoes significant conformational reorganization upon activation by relocating completely to the A1-domain. The conformational transition led to the exposure of the Tyr555-Asp569 loop and the surrounding region in the A2 domain. While the proposed linker peptide conformation is predictive in nature and warrants further experimental validation, the observed conformational differences between the zymogen and activated forms may explain and support the large body of experimental data that implicated the critical importance of the cleavage of the peptide bond between the Arg372 and Ser373 residues for the full co-factor activity of fVIII.

What causes the enhancement of activity of factor VIIa by tissue factor

inhibition of the tissue factor pathway by tissue factor pathway inhibitor. Proc Natl Acad Sci USA 2006; 103: 3106–11. 14 Martinuzzo M, Iglesias Varela ML, Adamczuk Y, Broze GJ, Forastiero R. Antiphospholipid antibodies and antibodies to tissue factor pathway inhibitor in women with implantation failures or early and late pregnancy losses. J Thromb Haemost 2005; 3: 2587–9. 15 Backos M, Rai R, Baxter N, Chilcott IT, Cohen H, Regan L. Pregnancy complications in women with recurrent miscarriage associated with antiphospholipid antibodies treated with low dose aspirin and heparin. Br J Obstet Gynaecol 1999; 106: 102–7. 16 Rai R, Cohen H, Dave M, Regan L. Randomised controlled trial of aspirin and aspirin plus heparin in pregnant women with recurrent miscarriage associated with phospholipid antibodies (or antiphospholipid antibodies). BMJ 1997; 314: 253–7. 17 Dolitzky M, Inbal A, Segal Y, Weiss A, Brenner B, Carp H. A randomized study of thromboprophylaxis in women with unexplained consecutive recurrent miscarriages. Fertil Steril 2006; 86: 362–6. 18 Brenner B, Hoffman R, Carp H, Dulitsky M, Younis J. Efficacy and safety of two doses of enoxaparin in women with thrombophilia and recurrent pregnancy loss: the LIVE-ENOX study. J Thromb Haemost 2005; 3: 227–9. 19 Aharon A, Lanir N, Drugan A, Brenner B. Placental TFPI is decreased in gestational vascular complications and can be restored by maternal enoxaparin treatment. J Thromb Haemost 2005; 3: 2355–7. 20 van t Veer C, Golden NJ, Kalafatis M, Mann KG. Inhibitory mechanism of the protein C pathway on tissue factor-induced thrombin generation. Synergistic effect in combination with tissue factor pathway inhibitor. J Biol Chem 1997; 272: 7983–94.

Structural insights into the interaction of blood coagulation co-factor VIIIa with factor IXa: a computational protein-protein docking and molecular dynamics refinement study.

Coagulation factor X (FX) zymogen activation by factor IXa (FIXa) enzyme plays a critical role in the middle-phase of coagulation cascade. The activation process is catalytically inert and requires FIXa binding and complex formation with co-factor VIIIa (FVIIIa). In order to understand the structural details of the FVIIIa:FIXa complex, we employed knowledge-driven protein-protein docking and aqueous-phase MD refinement methods to develop a stable structural complex between FVIIIa and FIXa. The model shows that all four domains of FIXa wrap across FVIIIa that spans the co-factor binding surface of A2, A3 and C1 domains. The region surrounding the 558-helix of the A2-domain of FVIIIa is predicted to be the key interaction site with the helical segments of Lys293-Lys301 and Asp332-Arg338 residues of the serine-protease domain of FIXa. The hydrophobic helical stack between the GLA and EGF1 domains of FIXa is predicted to be primary interacting region with the A3-C2 domain interface of FVIIIa.

Mutagenic significance of proton acidities in methylated guanine and thymine bases and deoxynucleosides: a theoretical study

Proton changes have been advanced as being the key molecular basis for the mutagenecity of alkylated DNA bases and nucleosides, leading to questions as to which protons are involved and whether the protic changes are tautomeric shifts or abstractions. This semiempirical molecular orbital study seeks to clarify the issue by examining the various possibilities open for these protic changes in a number of methylated guanines and thymines and their deoxynucleosides. Proton shifts leading to tautomer formation are not predicted as being thermodynamically favourable in most cases. The most feasible proton abstractions are predicted to involve the Watson-Crick protons in all cases, which corroborates Watson-Crick proton loss as providing the key molecular basis for the induction of point mutations. The calculated proton acidities correlate well with experimental data. The gas-phase deprotonation enthalpies for a number of alkylated nucleosides are found to correlate linearly with the solvent-phase pK(a) values. The theoretically calculated enthalpies in a simulated aqueous solvent phase of the deprotonation reactions of various nucleic acid bases are also found to have good linear correlations with experimental pK(a) values. The consensus of these calculations is that O-6-alkyldeoxyguanosines, and O-2- and O-4-alkyldeoxythymidines would be mutagenic while N-7-alkyldeoxyguanosines would not be mutagenic (as experiment indicates). The untested N-3-methyldeoxyguanosine is predicted to be mutagenic

Role of hydrophobic mutations on the binding affinity and stability of blood coagulation factor VIIIa: a computational molecular dynamics and free-energy analysis.

Factor VIIIa is a non-covalently bound hetero-trimer among A1, A2 and A3-C1-C2 domains and an essential co-factor for factor IXa enzyme during proteolytic activation of factor X zymogen. The relatively weak interactions between A2 and the interface A1/A3 domains dampen the functional stability of FVIIIa in plasma and results in rapid degradation. We studied the mutational effect of three charged residues (Asp519, Glu665 and Asp666) to several hydrophobic residues by molecular dynamics simulations. Analysis of the binding free energy by MM-PBSA and MM-GBSA methods shows that the mutation of Asp519 and Glu665 residues to either Val or Ala enhance the A2 domain binding affinity in agreement with the experimental site-specific mutagenesis data. Mutation of Asp666 to Val, Tyr, Met and Phe showed largest improvement in the A2-domain binding among the eight hydrophobic mutants studied. Our studies suggest that the enrichment of hydrophobic interactions in the buried surface regions of A2 domain plays crucial role in improving the overall stability of FVIIIa.

A semi-empirical SCF-MO study on the base-pairing properties of 8-oxopurines: Significance for mutagenicity

C8-Oxidised purines like 7-hydro-8-oxoguanine (8OG) and 7-hydro-8-oxoadenine (8OA) are known as products of oxidative DNA damage. Semiempirical molecular orbital calculations at the PM3 SCF-MO level are used to investigate the base-pairing properties of these bases in an attempt to understand their mutagenic properties. A detailed analysis of the base-pairing properties of these bases leads to an identification of the most probable pairing schemes involved in mutagenic base-mispairing. It is suggested that both bases are capable of inducing transversional as well as transitional mutations via base-mispairing. The results presented are largely in consonance with available experimental reports.

Deglycosylation of alkylated nucleosides: a molecular orbital study

The glycoside bond in alkylated nucleosides is known to be more stable for