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Protein Folding De novo Protein Design
Ranjit Ranbhor Soumendra Rana Anil Kumar Deepa Pednekar Kirti Patel Abhijit Tendulkar Sourav Das
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B.Pharm., College of Pharmacy, Nasik M.S. (Pharm), NIPER,Changdigarh
Computational Design of Heterochiral Proteins.
Stereochemistry could be a powerful variable for conformational tune up of polypeptides for de novo design. We have established that indeed a vast and essentially untapped potential exists for de novo design based on stereo chemical engineering of peptide structure. We take up here a larger question of stereochemistry-to-conformation relationship in polypeptide structure and approach a possible practical computational method for design of “heterochiral” folds at level of polypeptide stereochemistry.
Contact: School of Biosciences and
Bioengineering, IIT Bombay
B.Sc. , S.V.M College, Orissa M.Sc. (Organic Chemistry), Ravenshaw College, Orissa.
Peptide Molecular Folds of customized form and Function
Nature extracts phenomenal purchase from an alphabet of stereochemically frozen composition. The bonanza could be further extended by artificially restoring the molecular alphabet to its stereochemical parity. Recruitment of residue stereochemistry as an additional, higher level, sequence variable promises to multiply the polypeptide conformational template for de novo design, with the added bonus that it may be possible to customize molecular morphologies based on stereospecific folding of stereochemically programmed heterochiral polypeptides. With the lifting of stereochemical degeneracy in Nature’s building block alphabet, it may be possible to bridge the gulf between what is possible biologically and what has been accomplished artificially.
Contact: Department of Chemistry,
IIT Bombay
http://homepages.iitb.ac.in/~soumendra
Anil Kumar
B.Sc. , IGNOU, Patna (Bihar) M.Sc. (Organic Chemistry), University of Delhi.
De Novo Design of Proteins Diversified in Molecular Tacticity
We are working on De Novo Protein Design diversifying the molecular tacticity. Indeed, de novo design has two complimentary objectives; design of unknown or novel structures and test of underlying principles. Currently I am working on the studies involving The Role of Chain Stereochemistry in the protein conformational design and mapping Elementary Reaction Paths in protein folding. Besides this, I am also working on the Stereochemical Reengineering in heterotactic polypeptides in Form and Chemical Engineering in Function.
Contact: Department of Chemistry,
IIT Bombay
B.Pharm., C.U.Shah College of Pharmacy, Mumbai M.Pharm. (Medicinal Chemistry), UDCT, Mumbai
Symmetry and Stereochemistry in Protein Structure, Function and Design
Protein structures are fundamentally asymmetric given asymmetry of the monomer building blocks always L-configurational in structure. But symmetry can be functionally critical in phenomena like allostery, catalysis and multivalent binding and is achieved in protein structures by self-assembly in cyclic, dihedral or icosahedral symmetry. Symmetric proteins often communicate through interfaces that show an interplay of different physicochemical forces. The underlying principles evoke interest for possible application in de novo design of higher order structures by self-assembly of simple building blocks. We here make use of evolutionary methods as a guiding tool for design of protein interfaces for self assembling peptides.
Contact: School of Biosciences and
Bioengineering, IIT Bombay
B.Sc. , L. V. H. College, Nasik M.Sc. (Organic Chemistry), R. Y. T. College, Pune University.
De novo design of Zinc peptides diversified in molecular tacticity
The design and synthesis of new functional metalloproteins are some of the current topics in protein engineering. The successful design of metalloproteins significantly contributes to the understanding of fundamental principles in chemistry and biology and also provides an economic alternative for biotechnological applications. Our approach to this subject is through de novo design of peptides with a backbone chain stereochemistry as a variable. We aim to harness Zinc as an element to control conformation and impart function. Zinc is a versatile element playing both structural and functional roles in protein structure. Combining evolutionary searches and rational design methods, we are embarked on design of molecular systems with catalytic properties.
Contact: Department of Chemistry,
IIT Bombay
PROJECT STAFF
B.E. (Computer Engineering),
Protein Engineering Software
Contact: Department of Chemistry,
IIT Bombay
MSc STUDENT
B.Sc. Hons. (Chemistry), Sri Venkateswara College (University of Delhi)
Molecular Recognition in Protein Self-Assembly We are using concepts and algorithms from computational geometry, computer graphics and machine perception in tandem with chemical concepts to develop tools for estimating relative contributions of shape and different physico-chemical property complementarities at the interface that could be crucial for protein-protein association, self-recognition and specific patterns of binding. Our findings will augment the de-novo protein design efforts in our lab by helping us build software tools that could aid design self-associating mini-proteins.
Contact: Department of Chemistry,
IIT Bombay
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