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12 results on '"Pradhan, Mohan R."'

3. Incorporation of Putative Helix-Breaking Amino Acids in the Design of Novel Stapled Peptides: Exploring Biophysical and Cellular Permeability Properties

Author

Partridge, Anthony W., primary, Kaan, Hung Yi Kristal, additional, Juang, Yu-Chi, additional, Sadruddin, Ahmad, additional, Lim, Shuhui, additional, Brown, Christopher J., additional, Ng, Simon, additional, Thean, Dawn, additional, Ferrer, Fernando, additional, Johannes, Charles, additional, Yuen, Tsz Ying, additional, Kannan, Srinivasaraghavan, additional, Aronica, Pietro, additional, Tan, Yaw Sing, additional, Pradhan, Mohan R., additional, Verma, Chandra S., additional, Hochman, Jerome, additional, Chen, Shiying, additional, Wan, Hui, additional, Ha, Sookhee, additional, Sherborne, Brad, additional, Lane, David P., additional, and Sawyer, Tomi K., additional

Published
2019
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6. Small Molecules Targeting the Inactive Form of the Mnk1/2 Kinases

Author

Kannan, Srinivasaraghavan, primary, Pradhan, Mohan R., additional, Cherian, Joseph, additional, Joseph, Thomas L., additional, Poh, Zhi Ying, additional, Hai Yan, Yang, additional, Melvyn, Ho, additional, Boping, Liu, additional, Jeffrey, Hill, additional, Nacro, Kassoum, additional, and Verma, Chandra S., additional

Published
2017
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12. The interfacial character of antibody paratopes: analysis of antibody-antigen structures.

Author

Minh N. Nguyen, Pradhan, Mohan R., Verma, Chandra, and Pingyu Zhong

Subjects
*COMPUTATIONAL biology, *IMMUNE complexes, *HYDROGEN bonding, *IONIC interactions, *EPITOPES, *VAN der Waals forces
Abstract

In this study, computational methods are applied to investigate the general properties of antigen engaging residues of a paratope from a non-redundant dataset of 403 antibody-antigen complexes to dissect the contribution of hydrogen bonds, hydrophobic, van der Waals contacts and ionic interactions, as well as role of water molecules in the antigen-antibody interface. Consistent with previous reports using smaller datasets, we found that Tyr, Trp, Ser, Asn, Asp, Thr, Arg, Gly, His contribute substantially to the interactions between antibody and antigen. Furthermore, antibody-antigen interactions can be mediated by interfacial waters. However, there is no reported comprehensive analysis for a large number of structured waters that engage in higher ordered structures at the antibody-antigen interface. From our dataset, we have found the presence of interfacial waters in 242 complexes. We present evidence that suggests a compelling role of these interfacial waters in interactions of antibodies with a range of antigens differing in shape complementarity. Finally, we carry out 296835 pairwise 3D structure comparisons of 771 structures of contact residues of antibodies with their interfacial water molecules from our dataset using CLICK method. A heuristic clustering algorithm is used to obtain unique structural similarities, and found to separate into 368 different clusters. These clusters are used to identify structural motifs of contact residues of antibodies for epitope binding. [ABSTRACT FROM AUTHOR]

Published
2017
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