Computer Simulation, Protein Structure Homology Modeling Methods And Conotoxins With Calcium Channel Interaction

N-type voltage-gated calcium channels are membrane-bound proteins involved in neurotransmitter release from neurons. The channel consists of several protein subunits but it is the α1 subunit which contains both voltage sensor and the Ca2+ selective pore. The primary sequence of this subunit has been reported and has been proposed to consists of four repeated domains(I-Ⅳ), each of which is suggested to contain six transmembrane regions(S1-S6). The region S4 is highly positively charged and is thought to form the voltage sensor. There is an additional region (P region) between S5 and S6 which is thought to form at least part of the pore region of the channel. N-type calcium channels are selectively blocked by a number of small peptide neurotoxin, the ω-conotoxin. The three-dimensional structures of several of these have been solved by 2D NMR techniques. It is generally thought that these toxin occlude the pore, although this has not been proved. The P region of domain Ⅲ (Ⅲ P region) has been shown to be the principle binding region for conotoxin. In this paper, we construct the model of Ⅲ P region using the graphic molecular modeling program. To gain a better understanding on the mechanism of the channel blockade, we present the plausible binding model of ω -conotoxin GVⅠA, MVⅡA and SO3 to Ⅲ P region by using an automated docking program. In our model, the interactions with calcium channel of GVIA and MVⅡA maybe not identical, but the interactions with calcium channel of MVⅡA and SO3 are probably similar. The role of the key residues of these conotoxins have been elucidated.Pinellin is a plant protein with a molecular weight about 48kd, and is isolated from the juice of the Chinese medical herb pinellia(pinellina ternate.breit.), and it consists of several subunits. Pinellin can be used as an abortifacient protein for terminating early pregnancy of mice. Pinellin is also a plant lectin, as it exhibits a specific hemagglutinating activity to rabbit erythrocytes at a concentration as low as 2ug/ml. In this paper, we extract pinellin from pinellina terbate.breit. Up to now, x-ray diffraction technology is the most powerful method for investigating three-dimensional structure of aprotein. To investigate the three-dimensional structure of Pinellin and elucidate the relationship between the structure and function of Pinellin, we have an effort to obtain the crystal of Pinellin. Experiments of crystal growth are carried out by using hanging drop vapor diffusion method. After a week, crystals are obtain from the solution containing PEG-4000 at pH 7.5.The rate at determination of protein and nucleic acid sequences has increased dramatically. Structural information from x-ray crystallographic or NMR results, on the other hand, is obtained much more slowly. Because of the disparate rates of sequence and structure determination, there are many proteins for which sequence information is known but the three-dimensional structure is not. Homology modeling of protein structure is become a focus of structural biology. Many programs of homology modeling have been developed, and Homology and Modeler are two frequently used homology modeling programs. Homology is a computer program package that helps people build the structure of a protein when only its amino acid sequence and the complete atomic structure of at least one other reference protein are known, and it is a manual modeling program. Modeler is an automated homology modeling scheme designed to simultaneously combine information from the sequence alignment and the structures of multiple reference proteins. It derives 3D protein models without the time consuming separate stages of core region identification and loop region building or searching that are inherent to manual homology modeling schemes. Who is better, or which one should we choose between the two programs? Sometimes we must answer this question. To answer this question ,we must know the deviations that the two programs bring out. For this propose, we select three proteins with their structures been known as modeling object. These proteins are Integrin CR3 A domain, Cyanidium caldarium phycocyanin and Winged bean albumin I. We construct the structures of the three proteins using the Homology and Modeler program, and compare each modeled structure with real structure respectively. We know the limits of the two methods from the results of structure comparison.