Influence of thermal motion on 1H chemical shifts in proteins: the case of bovine pancreatic trypsin inhibitor

Simulation of oligopeptide dynamics and folding. The use of NMR chemical shifts to analyse the MD trajectories

In this paper, a simulation of the folding process, based on a random perturbations of the phi, psi, chi1 dihedral angles, is proposed to approach the formation at the atom level of both principal elements of protein secondary structure, the alpha-helix and the beta-hairpin structures. Expecting to understand what may happen in solution during the formation of such structures, the behaviour of large sets of random conformations that are generated for small oligopeptides was analysed. Different factors that may influence the folding (as conformational propensity, hydrophobic interactions and side-chain mobility) were investigated. The difference between the corresponding theoretical folding and the real conformational diversity that is observed in solution is appraised by a comparison between the calculated and observed NMR secondary chemical shifts. From this study it appears that hydrophobic interactions and mobility represent the principal factors that initiate folding and determine the observed hydrogen-bond pattern, which subsequently allows packing between the peptide side chains.

The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences

In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D-structures, are compared with the observed ones to appraise the behaviour of a known x-ray diffraction structure (of the bovine pancreatic trypsin inhibitor protein) when various molecular dynamics are applied. The results of a 200 ps molecular dynamics under various conditions are analysed and different ways to modify the molecular dynamics are considered. With the purpose of avoiding the time-consuming explicit representation of the solvent (water) molecules, an attempt was made to understand the role of the solvent and to develop an implicit representation, which may be refined. A simulation of hydrophobic effects in an aqueous environment is also proposed which seems to provide a better approximation of the observed solution structure of the protein.

The (1)H-NMR solution structure of the antitryptic core peptide of Bowman-Birk inhibitor proteins: a minimal canonical loop

Bowman-Birk inhibitor (BBI) proteins contain an inhibitory motif comprising a disulfide-bonded sequence that interacts with serine proteinases. Recently, a small 14-residue peptide from sunflowers (SFTI-1), which has potent anti-trypsin activity, has been found to have the same motif. However, this peptide also has an unusual head-to-tail cyclisation. To address the role of the core inhibitory sequence itself, we have solved the (1)H-NMR solution structure of an antitryptic 11-residue cyclic peptide that corresponds to the core reactive site loops of both SFTI-1 and Bowman-Birk inhibitor proteins. A comparison is made between the secondary chemical shifts found in this family and the canonical regions of several other inhibitors, giving some insight into relative flexibility and hydrogen bonding patterns in these inhibitors. The solution structure of the core peptide in isolation is found to retain essentially the same three-dimensional arrangement of both backbone and side chains as observed in larger antitryptic BBI and SFTI-1 fragments as well as in the complete proteins. The retention of the canonical conformation in the core peptide explains the peptids inhibitory potency. It therefore represents a minimization of both the BBI and SFTI-1 sequences. We conclude that the core peptide is a conformationally defined, canonical scaffold, which can serve as a minimal platform for the engineering of biological activity.