ÿþ<html> <head> <title>Michal Hammel Homepage</title> </head> <body text="#000000" bgcolor="#cccccc" link="#0000ee" vlink="#551a8b" alink="#ff0000"><BODY> <HR> <p align="center"><font face="Times New Roman" size="5" color="#234747"><strong>Research Interest</strong></font></p> <DIV align="justify"> <font size="3" face="Arial, Helvetica, sans-serif">My research interests are in the area of structural biology with a focus on the low resolution structures of protein revealed by Small Angle X-ray Scattering (SAXS) in the combination with different approaches of molecular dynamics simulations. Small-angle X-ray scattering (SAXS) is an effective method to investigate the low-resolution structure of proteins and his complexes at nearly physiological condition. SAXS not only provides low resolution three-dimensional models of particle shapes but yields answers to important functional questions. Thus, kinetic SAXS experiments allow one to analyze structural changes in response to variations in external conditions, protein-protein and protein-ligand interactions, and to study kinetics of assembly/dissociation or folding/unfolding. Fundamental biological processes such as cell-cycle control, signalling, DNA duplication, gene expression and regulation, some metabolic pathways, depend on supra-molecular assemblies and their changes over time. The intrinsic limitation of the SAXS to a low resolution can be overcome by the combined use of data at the atomic scale provided for example by X-ray diffraction and permitted to investigate not only the overall shapes in solution but to propose a model of the whole molecule at the atomic scale. The originality of this method is that it can provide structural information on molecules exhibiting some intrinsic disorder, flexibility or heterogeneity, what usually constitute a major obstacle for the other structural methods like X-ray crystallography, NMR and EM. </font> </DIV> <CENTER> <p><img src="video.gif" width="250" height="200"></p> <DIV align="justify"> <font size=2 face="Geneva, Arial, Helvetica, sans-serif">Fig. 1: Solution structure of minicellulosome revealed by SAXS. (Hammel et al. PNAS - submitted) </font> </DIV> </font><a></A><a></a><a><a href="fts4fc.mpg"><font size="3" face="Times New Roman, Times, serif">(download mpg)</font></a></a></a></p><a> <BR> <DIV align="justify"> <font size="3" face="Arial, Helvetica, sans-serif"> Molecular dynamics (MD) is widely used for exploring conformational space. A common strategy is to perform the simulation at very high temperature (~1500K). The additional kinetic energy prevents the molecule getting stuck in a localized region of conformational space. Different conformations of the protein are registered at regular intervals from the trajectory for subsequent calculation of the theoretical SAXS profiles. The discrepancy between the theoretical SAXS profile and the experimental data enabled to chose the finite number of the conformations with the best fit. This best fit conformations corespond to the most probable protein confromation of the protein. </font> </DIV> </font> </DIV> <CENTER> <p><img src="fig2.jpg" width="800" height="800"></p> <DIV align="justify"> <font size=2 face="Geneva, Arial, Helvetica, sans-serif">Fig. 2: The three-dimensional arrangements of the cellulosome-like constructs in free and complexed states were investigated according to atomic models restored from SAXS data. a) Each graph present the comparison of fit-discrepancy for 15000 models with their RG values. (b) The best-fit models can be considered as the boarder conformations limiting the possible movements of the proteins in solution. </font></a></a></a></p><a> <BR> <CENTER> <p><img src="xynz2.gif" width="200" height="200"></p> <DIV align="justify"> <font size=2 face="Geneva, Arial, Helvetica, sans-serif">Fig. 3: MD simulation of XynZ cellulosome complex perfomed at 1500K </font><a></A><a></a><a><a href="xynz2.mpg"><font size="3" face="Times New Roman, Times, serif">(download mpg)</font></a></a></a></p><a> </CENTER> <DIV align="justify"> <font size="3" face="Arial, Helvetica, sans-serif"> Normal Mode simulation (NMA) is the commonly used and convenient method to provide the information on protein dynamics. It allows for reconstitution of the temporal evolution of a molecular system at high resolution, as it occurs in its natural environment. Combination of the SAXS with NMA enable us to determinate the precise atomic model of large protein and his complexes and consequently predict the dynamical properties in response to variations of external conditions. </font> </DIV> <CENTER> <p><img src="modus7_9.gif" width="150" height="258"></p> <DIV align="justify"> <font size=2 face="Geneva, Arial, Helvetica, sans-serif">Fig. 3: Dynamical properties of the complexed full length celulase revealed by Normal Mode Analysis (NMA) <i> <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15502162"> J Biol Chem. 2004 Oct 23 </A> </i> </font> </DIV> </font><a></A><a></a><a><a href="modus7_9.mpg"><font size="3" face="Times New Roman, Times, serif">(download mpg)</font></a></a></a></p><a> <CENTER> <HR> <BR> <p ALIGN="center"><a href="index.html"><img src="home_m.gif" alt="home_m.gif(206 bytes)" width="35" height="30" border="0"></a> <a href="index.html"><font size="3" color="#008000"></font></a></p> </body> </html>