Publications

Publications

Google Scholar Link

(Total number of citations >1750; h-index = 22; i10-index = 25)

Since 2011

37. Force Spectroscopy of the Plasmodium falciparum vaccine candidate circumsporozoite protein suggests a mechanically pliable repeat region
Aditya P. Patra, Shobhona Sharma*, and Sri Rama Koti Ainavarapu*
Journal of the Biological Chemistry Vol 292 (2017) p2110-2119 PDF

36. Mechanical Unfolding Studies on Single-Domain SUMO protein and Multi-Domain Periplasmic Binding Proteins
Hema Chandra Kotamarthi* and Sri Rama Koti Ainavarapu*
Biophysical Reviews and Letters Vol ??? (2017) p???-??? PDF

35. Small peptide binding stiffens the ubiquitin-like protein SUMO1
Hema Chandra Kotamarthi, Anju Yadav, and Sri Rama Koti Ainavarapu*
Biophysical Journal Vol 108, No 2 (2016) p360-367 PDF

34. Significance of 1B and 2B domains in modulating elastic properties of lamin A
Manindra Bera, Sri Rama Koti Ainavarapu, and Kaushik Sengupta
Scientific Reports 6:27879 (2015) p1-12 PDF

33. Characterization of unfolding mechanism of human lamin A Ig fold by single-molecule force spectroscopy – implications in EDMD
Manindra Bera, Hema Chandra Kotamarthi, Subarna Dutta, Angana Ray, Saptaparni Ghosh, Dhananjay Bhattacharyya, Sri Rama Koti Ainavarapu, and Kaushik Sengupta

Biochemistry Vol 53 (2014) p7247-7258 PDF

32. Mechanical Unfolding of Ribose Binding Protein (RBP) and Its Comparison with Other Periplasmic Binding Proteins (PBPs)
Hema Chandra Kotamarthi, Satya Narayan, and Sri Rama Koti Ainavarapu*
Journal of Physical Chemistry B Vol 118 (2014), No 39, p11449-11454 PDF

31. Ca2+ binding enhanced mechanical stability of an archaeal crystallin
Venkatraman Ramanujam, Hema Chandra Kotamarthi, Sri Rama Koti Ainavarapu*
PLOS ONE Vol 9, (2014), e94513 PDF

30. Preventing Disulphide Bond Formation Weakens Non-covalent Forces Among Lysozyme Aggregates
Vijay Kumar Ravi, Mohit Goel, Hema Chandra Kotamarthi, Sri Rama Koti Ainavarapu, and Rajaram Swaminathan*
PLOS ONE Vol 9 (2014), e87012 PDF

29. Multiple unfolding pathways of leucine binding protein (LBP) probed by single-molecule force spectroscopy (SMFS)
Hema Chandra Kotamarthi, Riddhi Sharma, Satya Narayan, Sayoni Ray, and Sri Rama Koti Ainavarapu*
Journal of the American Chemical Society Vol 135 (2013) p14768-14774 PDF

This article is highlighted in ‘JACS Editorial on ‘Protein Dynamics in Simulation and Experiment’. Link 

This paper is highlighted in ‘JACS Select issue 31: Protein Dynamics in Simulation and Experiment’ Online JACS Select Issue 31, December 2014. Link

It is also highlighted in ‘Spotlights on Recent JACS Publications’ of JACS, 2013, 135 (41), pp 15269: Pulling on a Protein To Map Its Unfolding Pathways. PDF

28. Single-molecule studies on polySUMO proteins reveal their mechanical flexibility
Hema Chandra Kotamarthi, Riddhi Sharma, and Sri Rama Koti Ainavarapu*
Biophysical Journal Vol 104, No 10 (2013) p2273-2281 PDF
This paper is one of the “TOP 20 Most Accessed Articles” in May-June 2013 from the Biophysical Journal website.

27. Iterative cloning, overexpression, purification and isotopic labeling of an engineered dimer of a Ca2+-binding protein of the bg crystallin superfamilyfrom Methanosarcina acetivorans
Venkatraman Ramanujam, K.V.R. Chary, and Sri Rama Koti Ainavarapu*
Protein Expression and Purification Vol 84 (2012) p116-122 PDF
This paper is in the “TOP 20 Hottest Articles in Biochemistry, Genetics and Molecular Biology of Protein Expression and Purification”, April-June 2012Link

26.  Ligand modulated parallel mechanical unfolding pathways of Maltose Binding Proteins (MBPs)
Vasudha Aggarwal, S. Rajendra Kulothungan, M.M. Balamurali, S.R. Saranya, Raghavan Varadarajan, and Sri Rama Koti Ainavarapu*
J. Biol. Chem. Vol 286, No 32 (2011) p28056-28065 PDF

Before 2011

25. Single-molecule force-clamp spectroscopy: Probing transition states of mechanically activated chemical reactions
Sri Rama Koti Ainavarapu*
ISRAPS Bulletin Vol 21 (2009) p32-39

24. A Single-Molecule Perspective on the Role of Solvent Hydrogen Bonds in Protein Folding and Chemical Reactions
Lorna Dougan, Sri Rama Koti AinavarapuGeorgi Genchev, Hui Lu and Julio M. Fernandez
Chem Phys Chem Vol 9 (2008) p2836-2847 PDF

23. Single-Molecule Force Spectroscopy Measurements of Bond Elongation during a Bimolecular Reaction
Sri Rama Koti Ainavarapu*Arun P. Wiita, Lorna Dougan, Einar Uggerud, and Julio M. Fernandez*
Journal of the American Chemical Society Vol 130 (2008) p6479-6487 PDF
This JACS paper on ‘Mechanochemistry’ has been mentioned in Research Highlights section of Nature (2008), 453, pp261: “Disulphide dichotimies” PDF

22. Dwell Time Analysis of a Single-Molecule Mechanochemical Reaction
Robert Szoszkiewicz, Sri Rama Koti AinavarapuArun P. Wiita, Raul Perez-Jimenez, Jose M. Sanchez-Ruiz, and Julio M. Fernandez
Langmuir Vol 24 (2008) p1356-1364. PDF

21. A Single-Molecule Assay to Directly Identify Solvent Accessible Disulfide Bonds and Probe Their Effect on Protein Folding
Sri Rama Koti Ainavarapu*, Arun P. Wiita, Hector H. Huang, and Julio M. Fernandez
Journal of the American Chemical Society Vol 130 (2008) p436-437 PDF

20. Time-resolved photoluminescence of terbium-doped microporous-mesoporous Zeotile-1 materials
C. Tiseanu, M.U. Kumke, V.I. Parvulescu, Sri Rama Koti Ainavarapu, B.C. Gagea and J.A. Martens
Journal of Photochemistry and Photobiology A: Chemistry Vol 187 (2007) p299-304 PDF

19. Contour Length and Refolding Rate of a Small Protein Controlled by Engineered Disulfide Bonds
Sri Rama Koti Ainavarapu, Jasna Brujic, Hector H. Huang, Arun P. Wiita, Hui Lu, Lewyn Li, Kirstin A. Walther, Mariano Carrion-Vazquez, Hongbin Li, and J.M. Fernandez
Biophysical Journal Vol 92, No 1 (2007) p225-233 PDF

18. Mechanical Unfolding Pathways of the Enhanced yellow Fluorescent Protein Revealed by Single Molecule Force Spectroscopy
Raul Perez-Jimenez, Sergi Garcia-Manyes, Sri Rama Koti Ainavarapu, and J.M. Fernandez
J. Biol. Chem. Vol 281, No 52 (2006) p40010-40014 PDF

17. Fingerprinting DHFR in Single-Molecule AFM Studies
Sri Rama Koti Ainavarapu, Lewyn Li, and J.M. Fernandez
Biophysical Journal Vol 91, No 5 (2006) p2009-2010 PDF

16. Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques
Arun P. Wiita, Sri Rama Koti Ainavarapu, Hector H. Huang, and J.M. Fernandez
Proc. Natl. Acad. Sci. (USA) Vol 103, No 19 (2006) p7222-7227 PDF
Commentary on this article is reported in PNAS(2006), 103, p7533: “Covalent chemistry on distended proteins” PDF

15. Ligand binding modulates the mechanical stability of dihydrofolate reductase (DHFR)
Sri Rama Koti Ainavarapu, Lewyn Li, Carmen L. Badilla, and J.M. Fernandez
Biophysical Journal Vol 89, No 5 (2005) p3337-3344 PDF

14. Photophysical Properties and Rotational Relaxation Dynamics of Neutral Red Bound to b-cyclodextrin
M.K. Singh, H. Pal, Sri Rama Koti Ainavarapu, and A.V. Sapre
J. Phys. Chem. A Vol 108, (2004) p1465-1474 PDF

13. Control of Coherence length and Aggregate size in the J-Aggregate of Porphyrin
Sri Rama Koti Ainavarapu,  Jharna Taneja, and N. Periasamy
Chemical Physics Letters Vol 375, No 1-2 (2003) p171-176 PDF

12. Time Resolved Fluorescence Spectroscopy: TRES and TRANES
N. Periasamy and Sri Rama Koti Ainavarapu
Proc. Indian Natl. Sci. Acad. Vol 69, No 1 (2003) p41-48 PDF

11. Self-Assembly of Template-Directed J-aggregates of Porphyrin
Sri Rama Koti Ainavarapu and N. Periasamy
Chemistry of Materials Vol 15, No 2 (2003) p369-371 PDF

10. TRANES Spectra of Fluorescence Probes in Lipid Bilayer Membranes: An Assessment of Population Heterogeneity and Dynamics
Ira, Sri Rama Koti Ainavarapu, G. Krishnamoorthy, and N. Periasamy
Journal of Fluorescence Vol 13, No 1 (2003) p95-103 PDF

9.  Time Resolved Area Normalized Emission Spectroscopy (TRANES) of DMABN Confirms Emission from Two States
Sri Rama Koti Ainavarapu and N. Periasamy
Research on Chemical Intermediates Vol 28, No 7-9 (2002) p831-836 PDF

8.  Cyanine induced Aggregation in meso-tetrakis(4-sulphonatophenyl) Porphyrin Anions
Sri Rama Koti Ainavarapu and N. Periasamy
Journal of Materials Chemistry Vol 12, No 8 (2002) p2312-2317 PDF

7.  Time Resolved Fluorescence Spectroscopy: TRES vs TRANES
N. Periasamy and Sri Rama Koti Ainavarapu
ISRAPS Bulletin Vol 12, No 1-4 (2001) p26-29 PDF

6.  Application of Time Resolved Area Normalized Emission Spectroscopy (TRANES) to multi-component systems
Sri Rama Koti Ainavarapu and N. Periasamy
J. Chem. Phys. Vol 115, No 15 (2001) p7094-7099 PDF

5.  TRANES analysis of the Fluorescence of Nile Red in Organized Assemblies Confirms Emission from Two species
Sri Rama Koti Ainavarapu and N. Periasamy
Proc. Indian Acad. Sci. (Chem. Sci.) Vol 113, No 2 (2001) p157-163 PDF

4.  Time-Resolved Area-Normalized Emission Spectroscopy (TRANES): A Novel Method for Confirming Emission from Two Excited States
Sri Rama Koti Ainavarapu, M.M.G. Krishna, and N. Periasamy
J. Phys. Chem A 105 (2001) p 1767-1771. PDF
Our TRANES work has been a part of the Principles of Fluorescence Spectroscopy,

3rd edition, by J.R. Lakowicz, chapter 7, p237-276. PDF

3.  Photophysics of some styryl thiazolo quinoxaline dyes in organic media

Sri Rama Koti AinavarapuB. Bhattacharjee, N.S. Haram, Ranjan Das, N. Periasamy, N.D. Sonawane, and D.W. Rangnekar
Journal of Photochemistry and Photobiology A: Chemistry Vol 137 No 2-3 (2000) p115-123 PDF

2.  Solvent Exchange in Excited-State Relaxation in Mixed Solvents
Sri Rama Koti Ainavarapu and N. Periasamy
Journal of Fluorescence Vol 10, No 2 (2000) p177-184 PDF

1.  NMR studies on truncated sequences of human telomeric DNA: observation of a novel A-tetrad
Prasanta K. Patel, Sri Rama Koti Ainavarapu, and R.V. Hosur
Nucleic Acids Research Vol 27, No 19 (1999) p3836-3843 PDF

 

 

 

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