Thenmalarchelvi Rathinavelan

Molecular Biophysics

  1. Rathinavelan, T., Tang, C. and De Guzman, R.N. (2011), “Characterization of the Interaction between the Salmonella Type III Secretion System Tip Protein SipD and the Needle Protein PrgI by Paramagnetic Relaxation Enhancement”, J. Biol. Chem. 286, 4922-30

  1. Lim, K.H., Nagchowdhuri P., Rathinavelan, T. and W. Im (2010) "NMR Characterization of Hydrophobic Collapses in Amyloidogenic Partially Folded States and Their Implications for Protein Misfolding and Amyloid Formation", Biochem. Biophys. Res. Commun. 396, 800-05

  1. Rathinavelan, T., Zhang, L., Picking, W.L., Weis, D.D., De Guzman, R.N. and Im, W. (2010), “A Repulsive Electrostatic Mechanism for Protein Export through the Type III Secretion Apparatus”, Biophy. J. 98, 452-61 (Cover page article) (Highlighted paper)

  1. Rathinavelan, T. and Im, W. (2008), “A Novel Strategy to Determine Protein Structures using Exclusively Residual Dipolar Coupling”, J. Comput. Chem. 29, 1640-49

  1. Wang, Y., Ouellette, A.N., Egan, C.W., Rathinavelan, T., Im, W. and De Guzman, R.N. (2007),Differences in the Electrostatic Surfaces of the   Type III Secretion Needle Proteins”, J. Mol. Biol., 371, 1304-14

  1. Rathinavelan, T. and Im, W. (2007), “Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination”, J. Comput. Chem., 28, 1858-64

  1. Rathinavelan, T. and Yathindra, N. (2006), “Base triplet nonisomorphism strongly influences DNA triplex conformation: effect of nonisomorphic G* GC and A* AT triplets and bending of DNA triplexes”, Biopolymers, 82, 443-61

  1. Rathinavelan, T. and Yathindra, N. (2005), “Molecular dynamics structures of peptide nucleic acid x DNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene: Stereochemical rationale for the low affinity of PNA in the presence of an A.C mismatch”, FEBS J., 272, 4055-70

  1. Thenmalarchelvi, R. and Yathindra, N. (2005), “New insights into DNA triplexes: Residual twist and radial difference as measures of base triplet non-isomorphism and its implication to sequence dependent non-uniform DNA triplex”, Nucleic Acids Res., 35, 43-55

  1. Xodo, L.E, Rathinavelan, T., Quadrifoglio, F., Manzini, G., and Yathindra, N. (2001), “Targeting neighbouring poly(purine.pyrimidine) sequences located in the human bcr promoter by triplex-forming oligonucleotides”, Eur. J. Biochem., 268, 656-64

Peer-reviewed Journals

Book Chapters

  1. Rathinavelan, T. and Im, W. (2010),A computational approach to explore protein translocation through type III secretion apparatus”, In Quantum Bio-Informatics: From Quantum Information to Bio-Informatics, Eds. L. Accardi, W. Freudenberg, and M. Ohya  26, 453-63 

  1. Thenmalarchelvi, R. and Yathindra, N. (2003), ‘“Residual” Hoogsteen twist as a measure of nonisomorphism in DNA base triplets: Implications to sequence dependent DNA triplexes’, Recent Trends in Biophysical Research, Eds. Maiti, M., Suresh Kumar, G. and Das, S., 17-24, Publishers: Double A Work Station, Kolkata, India


From UM, IBAB & KU

  1. Patro, L.P.P.*, Kumar, A.*, Kolimi, N.* and Rathinavelan, T. (2017), 3D-NuS: A Web Server for Automated Modeling and Visualization of non-canonical 3-Dimensional Nucleic Acid Structures” . J Mol Biol., 429,2438-2448. (*Equal contribution)

  1. Kolimi, N.*, Ajjugal. Y* and Rathinavelan, T. (2017), A B-Z junction induced by an A … A mismatch in GAC repeats in the gene for cartilage oligomeric matrix protein promotes binding with the hZαADAR1 protein. J Biol Chem. 292, 18732-18746 (*Equal contribution) 

  1. Sachdeva, S.*, Palur, R.V.*, Sudhakar, K.U.* and Rathinavelan, T. (2017),E. coli group I capsular polysaccharide exportation nanomachinary as an antivirulent target in the perspective of emerging antimicrobial resistance”. Front Microbiol 8:70. doi: 10.3389/fmicb.2017.00070. eCollection 2017. (*Equal contribution)

  1. Goldsmith, G., Rathinavelan, T. and Yathindra N. (2016), “Selective Preference of Parallel DNA Triplexes is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity Between the G*GC and T*AT triplets”, PLoS One 11(3), e0152102 (IF: 3.234)

  1. Sachdeva, S.*, Kolimi, N.*, Nair, S.A.* and Rathinavelan, T. (2016), Key Diffusion Mechanisms Involved in Water Conduction of Wzi, Sci.  Rep. 28157. doi: 10.1038/srep28157 (*Equal contribution) (IF: 5.2)

  1. Kunduru, B.R.*, Nair, S.N.* and Rathinavelan, T. (2016), EK3D: an E. coli K antigen 3-Dimensional Structure Database, Nucleic Acids Res. 44 (D1), D675-D681 (*Equal contribution)  (IF: 9.112)

  1. Khan, N.*, Kolimi, N* and Rathinavelan, T.* (2015), Twisting Right To Left: A…A Mismatch In A CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation, PLoS Comput. Biol. Published: April 13, 10.1371/journal.pcbi.1004162 (*Equal contribution)  (IF: 4.829)

  1. Rathinavelan, T., Lara-Tejero, M., Lefebre, M., Chatterjee, S., McShan, A.C., Guo, D-C., Tang, C., Galan, J.E. and De Guzman, R.N. (2014),NMR Model of PrgI-SipD Interaction and its Implications in the Needle-Tip Assembly of the Salmonella Type III Secretion System”, J. Mol. Biol. 426, 2958-69  (Continuation of KU Work) (IF: 3.959)

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