Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23–230) as detected by [1H, 15N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn2+-binding to the octarepeat motif.

We report the molecular characterization of β-1,3-glucanase-producing Bacillus amyloliquefaciens-an endophyte of Hevea brasiliensis antagonistic to Phytophthora meadii. After cloning and sequencing, the β-1,3-glucanase gene was found to be 747 bp in length. A homology model of the β-1,3-glucanase protein was built from the amino acid sequence obtained upon translation of the gene. The target β-1,3-glucanase protein and the template protein, endo β-1,3-1,4-glucanase protein (PDB ID: 3o5s), were found to share 94% sequence identity and to have similar secondary and tertiary structures. In the modeled structure, three residues in the active site region of the template-Asn52, Ile157 and Val158-were substituted with Asp, Leu and Ala, respectively. Computer-aided docking studies of the substrate disaccharide (β-1, 3-glucan) with the target as well as with the template proteins showed that the two protein-substrate complexes were stabilized by three hydrogen bonds and by many van der Waals interactions. Although the binding energies and the number of hydrogen bonds were the same in both complexes, the orientations of the substrate in the active sites of the two proteins were different. These variations might be due to the change in the three amino acids in the active site region of the two proteins. The difference in substrate orientation in the active site could also affect the catalytic potential of the β-1,3 glucanase enzyme.

Factor XIII (FXIII) is a transglutaminase involved in blood coagulation. The enzyme is activated by thrombin cleaving the peptide bond R37-G38. A common mutation V34L found in FXIII has been correlated with protection from myocardial infarction. Also FXIII V34L is activated more quickly than the wild type. In the present study, FXIII (28-41) V34L mutant peptide bound to thrombin has been modeled and molecular dynamics simulations were carried out using Insight II. An average structure was calculated after simulation. The structure showed significant difference from the crystal structure of the wild type FXIII (28-37) peptide bound to thrombin. In the crystal structure the peptide adopts a folded conformation in such a way that the hydrophobic side chains of V29 and V34 occupy the apolar binding site of thrombin. The modeled V34L peptide adopts a significantly different conformation and only the bulkier L34 occupies the apolar binding site while V29 side chain is exposed to the bulk solvent. Hence, this may speed up the release of FXIII from thrombin after its activation.

Seminalplasmin (SPLN) is a 47-residue peptide (SDEKASPDKHHRFSLSRYAKLANRLANPKLLETFLSKWIGDRGNRSV) from bovine seminal plasma. It has broad spectrum antimicrobial activity, without any hemolytic activity. The 28-40 segment of SPLN with the sequence PKLLETFLSKWIG, designated as SPF, is the most hydrophobic stretch of SPLN and primarily responsible for the membrane-perturbing activity of SPLN. It was reported that SPF has a helical structure and the interchange of E5 and K10 residues disrupted the helical structure. The present paper reports a possible mechanism of disruption of the helical structure of SPF peptide during the interchange of E5 and K10 residues. The result is based on simulated annealing and molecular dynamics simulation studies on SPF and its four analogues with K10E, K10D, E5K, and E5K & K10E substitutions. It showed that K10 residue has a critical role in maintaining the highest helical content and the positions of charged residues are also very important for maintaining the helical structure of the SPF peptide. Formation of some new long-range hydrogen bonds and the rupture of some short-range hydrogen bonds involving the tenth residue led to the disruption of helical structure of SPF peptide when E5 and K10 residues are interchanged.

α-1,4-Amylase is one of the most important industrial enzymes and there is enormous interest in isolating α-1,4-amylase with better properties. The α-1,4-amylase producing endophytic Bacillus amyloliquefaciens was isolated and characterized from Hevea brasiliensis. The α-1,4-amylase gene after cloning and sequencing contained 1542 base pairs. A homology model of the α-1,4-amylase enzyme was built from the deduced amino acid sequence. The modelled and template α-1,4-amylase enzyme (PDB ID:3bh4) showed 97.7% sequence identity with similar secondary and tertiary structures. Computer aided docking studies of the substrate (maltotetraose) with the modelled as well as the template enzymes showed that although the binding energies were almost the same in both the complexes, the number of hydrogen bonds and van der Waals interactions in the active sites of the two enzymes were different. These variations might be due to the change in the amino acid residues of the active site regions of two enzymes. The mutated polar amino acids in the active site of modelled α-1,4-amylase favoured more hydrogen bond formation with the substrate. The difference in the active site interactions may improve the specificity of the enzyme and affect the catalytic potential of α-1,4-amylase.