|M. Madan Babu, PhD
Group Leader / Investigator
MRC-Laboratory of Molecular Biology
Hills Road, Cambridge CB2 2QH, United Kingdom
University of Cambridge
See new group page at: http://mbgroup.mrc-lmb.cam.ac.uk/
Last major modification to the contents below was made in 2002
My research interest is primarily in the area of Computational Molecular Biology, Computational Pathogenesis, Protein Structure Analysis and Biotechnology.
In all organisms, there are cascades of transcription factors that regulate each other in order to amplify or diversify the effect of a signal on gene regulation. This is true even in simpler organisms such as the prokaryote E. coli, where the most complex known cascade involves four levels of transcription factors. To gain insight into the evolution and organisation of the transcription factor regulatory network in E. coli, we have looked at the transcription factor regulatory network from a structural and functional perspective.
Transcription factors (TFs) and the regulated genes in an organism form a complex network, which plays a central role in the functioning of the organism. In this study, we have looked at the gene regulatory network from a structural, functional and an evolutionary perspective in E. coli and we have compared it independently with the transcription factor regulatory network in E. coli.
Bacterial lipoproteins and lipid modification are gaining importance owing to their essential nature, roles in pathogenesis and interesting commercial applications. We have created an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant molecular details. We are analysing the domain architecture in this important class of proteins to understand how they evolved.
Projects handled as an undergraduate:
The decapeptide (BOC - M - L - F -V - DP - A - L - V - V - F - OMe) was purified by HPLC and the purity was checked by a MALDI mass spectrometer. NMR experiments (TOCSY, NOESY and Temperature experiments) were conducted to get information on the structural features and the hydrogen bonding patterns. From the spectra, the distance restraints were derived and were used to build a model of the peptide. Molecular Dynamics Simulation using Insight II, was carried out with the above mentioned distance restraints. Structures with the least energy were chosen and checked for violation of restraints. Programs were written to check all these parameters. Finally, fifteen best structures were superimposed to get the representative structure and the RMSD was calculated.
The eight-stranded a /b barrel (TIM barrel) is by far the most common tertiary fold observed in high-resolution protein crystal structures. The members of this large family of proteins catalyze very different reactions. Such diversity in function has made this family an attractive target for protein engineering. Moreover, the evolutionary history of this protein family has been the subject of rigorous debate. Arguments have been made in favor of both convergent and divergent evolution. In my study, an analysis has been attempted on proteins which were found to have the a/b structural motif to study their structural features like conformational preferences, functional significance, topological features such as solvent accessibility, residue preference, salt bridges, sequence similarity and barrel geometry.
The TIM sequence from the P. falciparum genome was compared with the existing sequence characterized in Prof. Balaram's lab. The annotated sequence in the genome could not have been TIM because the active site residue was missing. By sequence analysis, a function for the "annotated TIM" was suggested. It was proposed to exist as a dimer without the TIM activity. The N-terminal region showed 100% sequence homology with an antigenic domain followed immediately by the predicted transmembrane helix. BLAST and PSI-BLAST programs were used for the analysis along with CLUSTALW for Multiple Sequence Analysis. Before the completion of this project, the sequence was replaced at the Sanger center. The new sequence also has anomalies in that it is unusually large and has a poly-Lysine stretch - characteristics unusual of TIM.
Upon an incidental observation of this type of a H-bond in a synthetic helical peptide, an analysis was proposed and carried out to check whether helices in naturally occurring proteins contained this type of a H-bond. A non-redundant high-resolution dataset of 61 proteins with resolution < 1.2 Å, was created and the helices were characterized according to the Phi-Psi values and helix length. Programs were written to extract helices with C-O distance < 4 Å. The H was fixed on the alpha Carbon, and the distance between the fixed H and the O was calculated. A cutoff of 3 Å was given. 16 proteins were found to fall in to this category. A careful stereochemical analysis of the helices was carried out and a striking observation was made. We are waiting for the dataset to become sufficiently large to carry out the same analysis so that the conclusions obtained can be generalized.
Bacterial growth curve, which is asymptotic after a certain period, was described using three different models, namely, Logistic model, Gompertz model and Richards model. Evaluating the mathematical parameters involved fitted the equations for these three models. This was done by applying the method of partial sums to the data containing the optical density values for different cell mass at different time intervals. The sum of square of residuals between the expected optical density values and the experimental values were calculated for each of these models. In the cases tested, the Logistic model was found to be the best fit for the growth curve of B. subtilis and was found to be easy to use. These results fit the data very well at 5% level for more than 70% of the readings.
Shigella apyrase or ATP diphosphohydrolase is a periplasmic virulence factor. Its primary structure is very similar to those of acid phosphatases indicating that it could have evolved from an ancestral acid phosphatase and belongs to the subgroup type 3A. We have analyzed the primary structure of Shigella apyrase in the light of the tertiary structure of Escherichia blattae acid phosphatase, reported this year. We propose that Shigella apyrase might belong to a new class of pyrophosphatases that might have emerged as one more variant from the family of acid phosphatases with specific advantages as a virulence factor to the pathogen.
Literature survey to collect information on the Cry gene family and DNA shuffling was collected and a project proposal to carry out the DNA shuffling of the cry proteins was written. Nucleotide sequence analysis of the Cry proteins was done to design degenerate primers.
Bacterial lipoproteins and lipid modification are gaining importance owing to their essential nature, roles in pathogenesis and interesting commercial applications. We have created an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility.
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