June 2002 Research Report


After a meeting with Rebecca on June 11, 2002, we decided that upon an order of importance for my SRP research which I pursued. The questions we wanted to answer include:


1)Using DALI (http://www.ebi.ac.uk/dali.html), can we identify other useful structures for superimposition other than the nitrogenase iron protein structure, 1n2c.pdb that Irmi used? DALI is a structural alignment database for similar structures with not necessarily a high sequence identity.


2)Is the nitrogenase based structure reasonable? Is is the best? Are there other protein homodimers or heterodimers that would be just as or more suitable for modeling the SRP:SRP receptor complex (see DALI)?


3)Check the hypothesized protein models with Molsurfer, looking for clashes or complementarity (electrostatic, hydrophobic) at the interface.


4)Add Mg2+ for this bound form to Ffh and FtsY. Add Mg2+/GTP for this bound form to Ffh and FtsY. Add Mg2+/GTPgS for this bound form to Ffh and FtsY. Do the apo-forms with no metal or cofactor clash? Could be okay if there is a confomation small change at the interface upon metal-cofactor binding. Place GTPgS with sup2pdbs onto GTP.


5)Check the metal-cofactor placements with Autogroup in Grid.


6)Check metal-cofactor bound forms with Molsurfer.


7)Minimize Mg2+, Mg2+-GTP, Mg2+-GTPgS protein-bound forms with Amber. Use Whatif to add polar hydrogens and Amber to add all other hydrogen atoms in parm94.dat.


8)Use UHBD to look at electrstatic interactions of the three forms.


9)Look at the UHBD results with Molsurfer with each of the three ligand bound. Are the electrostatic surfaces complementary?


10)Look at list of mutational data with Molsurfer. Where are these mutations? What would they be expected to affect: GTP-Mg2+ binding, interface, etc.?


DALI is a structural similarity alignment server (Liisa Holm Chris Sander, Protein Structure Comparison by Alignment of Distance Matrices, J. Mol. Biol. 233: 123-138, 1993). Their summary from their web page: With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional coordinates of each protein are used to calculate residue-residue (Calpha-Calpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g., hexapeptide-hexapeptide submatrices. Then, similar contact patterns in the two matrices are paired and combined into larger consistent sets of pairs. A Monte Carlo procedure is used to optimize a similarity score defined in terms of equivalent intramolecular distances. Several alignments are optimized in parallel, leading to simultaneous detection of the best, second-best and so on solutions. The method allows sequence gaps of any length, reversal of chain direction, and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic and identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions. An all-against-all alignment of over 200 representative protein structures results in an objective classification of known 3D folds in agreement with visual classifications. Unexpected topological similarities of biological interest have been detected, e.g., between the bacterial toxin colicin A and globins, and between the eukaryotic POU-specific DNA-binding domain and the bacterial lambda repressor.


Conferences:

I spent a day at EMBL for a minisymposium on Metabolic Networks- experimental and computational approaches on June 4th at EMBL which was held to evaluate the possibility of a new EMBL faculty in the field.


I presented a new poster of my work on the SRP project at the European Media Laboratory meeting enitled Building Protein-Protein Interaction Networks in Heidelberg held on June 20, 2002. Irmi was sick so we did not discuss the project. I showed the same poster as from Darmstadt and Huenfeld.


I also gave an 20 minute oral presentation on the SRP project at GPBM 2002: International Conference Genomics, Proteomics and Bioinformatics for Medicineheld on ship from Moscow to St. Petersburg, Russia from June 22-July 1, 2002. Dr. No from Korea (who worked with Scheraga) questioned why I had not included water in my minimizations and interface to fill holes. Hartmut Oschkinat questioned how good I thought my model was at 35-37% homology.







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