Publications

Dalal V, Golemi-Kotra D, Kumar P*. Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus. J. Chem. Inf. Model. 2022, 62, 10, 2409–2420

Dalal V*, Dhankhar P, Singh V, Rakhaminov G, Golemi-Kotra D, Kumar P*. Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus: Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MM. Protein J . 2021 Apr;40(2):148-165.

Dhankhar P, Dalal V, Golemi Kotra D, Kumar P*. In-silico approach to identify novel potent inhibitors against GraR of Staphylococcus aureus. Frontiers in Bioscience, Landmark, 25, 1337-1360, March 1, 2020

Jani, S, Sterzenbach K, Adatrao V, Tajbakhsh G, Mascher T*, Golemi-Kotra D*. Low phosphatase activity of LiaS and strong LiaR-DNA affinity explain the unusual LiaS to LiaR in vivo stoichiometry. BMC Microbiol, 2020 Apr 29;20(1):104.

Singh V, Dalal V, Dhankhar P, Rakhaminov G, Golemi Kotra D, Kumar P*. Molecular Docking and Simulation Study to Identify Novel Potent Inhibitors Against FmtA in Staphylococcus Aureus. SSRN, Elsevier, Feb 2020, Available at SSRN

Dalal V, Kumar P, Rakhaminov G, Qamar A, Fan X, Hunter H, Tomar S, Golemi-Kotra D* and Kumar P*. Repurposing an Ancient Protein Core Structure: Structural Studies on FmtA, a Novel Esterase of Staphylococcus aureus. . Mol. Biol. Jun 28. pii: S0022-2836(19)30408-5. doi: 10.1016/j.jmb.2019.06.019. [Epub ahead of print].

Tajbakhsh G. and Golemi-Kotra D*. The dimerization interface in VraR is essential for induction of the cell wall stress response in Staphylococcus aureus: a potential drugable target. BMC Microbiol. 2019 Jul 5;19(1):153.

Rahman MM, Hunter HN, Prova S, Verma V, Qamar A, Golemi-Kotra D*. The Staphylococcus aureus Methicillin Resistance Factor FmtA Is a D-Amino Esterase That Acts on Teichoic Acids. MBio. 2016 Feb 9;7(1). pii: e02070-15.
Highlighted in Faculty 1000 Prime by Yo Luo (University of Saskatchewan).

Singh S, Katiki, M. Gill P, Kumar P*, and Golemi-Kotra D*. Active Site Plasticity is Essential for Carbapenem-Hydrolyzing Class D β-Lactamase Catalysis as Revealed by OXA-58 Structural Studies. Antimicrob. Agents Chemother. 2015, 60, 75-86.

Patel, K and Golemi-Kotra, D*. Signaling Mechanism by the Staphylococcus aureus Two-Component System LytSR: Role of Acetyl Phosphate in Bypassing the Cell Membrane Electrical Potential Sensor LytS. F1000Research, 2015. Version 2. F1000Res. 4:79.

Muzamal U, Gomez D, and Golemi-Kotra D*. Diversity of two-component systems: insights into the signal transduction mechanism by the Staphylococcus aureus two-component system GraSR. F1000Research 2014, 3:252

Shala A, Patel K H, Golemi-Kotra D* and Audette G*. Expression, Purification, Crystallization and Preliminary X-ray Analysis of the Receiver Domain of the Staphylococcus aureus LytR Protein. October 2013. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Dec;69(Pt 12):1418-21. [Epub 2013 Nov 29]

Fridman M, Williams GD, Muzamal U, Hunter HN, Siu KW, Golemi-Kotra D*. Two unique phosphorylation-driven signaling pathways crosstalk in Staphylococcus aureus to modulate the cell wall charge: Stk1/Stp1 meets GraSR. Biochemistry. 2013, 52, 7975-86. [Epub, 2013 Oct 9].
Highlighted in Faculty 1000 Prime by Dr. Suzanne Walker (Harvard Medical School)

Leonard PG, Golemi-Kotra D, Stock AM. Phosphorylation-dependent conformational changes and domain rearrangements in Staphylococcus aureus VraR activation. Proc Natl Acad Sci U S A. 2013 May 21;110(21):8525-30. Epub 2013 May 6.

Rob T, Gill PK, Golemi-Kotra D, Wilson DJ. An electrospray ms-coupled microfluidic device for sub-second hydrogen/deuterium exchange pulse-labelling reveals allosteric effects in enzyme inhibition. Lab Chip. 2013 Feb 21. [Epub ahead of print]

Zhao Y, Verma V, Belcheva A, Singh A, Fridman M, Golemi-Kotra D. Staphylococcus aureus methicillin-resistance factor fmtA is regulated by the global regulator SarA. PLoS One. 2012;7(8):e43998. Epub 2012 Aug 30.

Qamar A, Golemi-Kotra D. Dual Roles of FmtA in Staphylococcus aureus Cell Wall Biosynthesis and Autolysis. Antimicrob Agents Chemother. 2012 Jul;56(7):3797-805. Epub 2012 May 7.

Belcheva A, Verma V, Korenevsky A, Fridman M, Kumar K, Golemi-Kotra D. Roles of DNA sequence and sigma A factor in transcription of the vraSR operon. J Bacteriol. 2012 Jan;194(1):61-71. Epub 2011 Oct 21.

Verma V, Testero SA, Amini K, Wei W, Liu J, Balachandran N, Monoharan T, Stynes S, Kotra LP, Golemi-Kotra D. Hydrolytic mechanism of OXA-58 enzyme, a carbapenem-hydrolyzing class D β-lactamase from Acinetobacter baumannii. J Biol Chem. 2011 Oct 28;286(43):37292-303. Epub 2011 Aug 31.

Liu YH, Belcheva A, Konermann L, Golemi-Kotra D. Phosphorylation-induced activation of the response regulator VraR from Staphylococcus aureus: insights from hydrogen exchange mass spectrometry. J Mol Biol. 2009 Aug 7;391(1):149-63. Epub 2009 Jun 9.

Belcheva A, Verma V, Golemi-Kotra D. DNA-binding activity of the vancomycin resistance associated regulator protein VraR and the role of phosphorylation in transcriptional regulation of the vraSR operon. Biochemistry. 2009 Jun 23;48(24):5592-601.

Belcheva A, Golemi-Kotra D. A close-up view of the VraSR two-component system. A mediator of Staphylococcus aureus response to cell wall damage. J Biol Chem. 2008 May 2;283(18):12354-64. Epub 2008 Mar 7.

Holtzman JH, Woronowicz K, Golemi-Kotra D, Schepartz A. Miniature protein ligands for EVH1 domains: interplay between affinity, specificity, and cell motility. Biochemistry. 2007 Nov 27;46(47):13541-53. Epub 2007 Nov 1.

Fan X, Liu Y, Smith D, Konermann L, Siu KW, Golemi-Kotra D. Diversity of penicillin-binding proteins. Resistance factor FmtA of Staphylococcus aureus. J Biol Chem. 2007 Nov 30;282(48):35143-52. Epub 2007 Oct 9.

Thomas VL, Golemi-Kotra D, Kim C, Vakulenko SB, Mobashery S, Shoichet BK. Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase. Biochemistry. 2005 Jul 5;44(26):9330-8.

Golemi-Kotra D, Meroueh SO, Kim C, Vakulenko SB, Bulychev A, Stemmler AJ, Stemmler TL, Mobashery S. The importance of a critical protonation state and the fate of the catalytic steps in class A beta-lactamases and penicillin-binding proteins. J Biol Chem. 2004 Aug 13;279(33):34665-73. Epub 2004 May 19.

Golemi-Kotra D, Mahaffy R, Footer MJ, Holtzman JH, Pollard TD, Theriot JA, Schepartz A. High affinity, paralog-specific recognition of the Mena EVH1 domain by a miniature protein. J Am Chem Soc. 2004 Jan 14;126(1):4-5.

Golemi-Kotra D, Cha JY, Meroueh SO, Vakulenko SB, Mobashery S. Resistance to beta-lactam antibiotics and its mediation by the sensor domain of the transmembrane BlaR signaling pathway in Staphylococcus aureus. J Biol Chem. 2003 May 16;278(20):18419-25. Epub 2003 Feb 18.

Maveyraud L, Golemi-Kotra D, Ishiwata A, Meroueh O, Mobashery S, Samama JP. High-resolution X-ray structure of an acyl-enzyme species for the class D OXA-10 beta-lactamase. J Am Chem Soc. 2002 Mar 20;124(11):2461-5.

Meroueh SO, Roblin P, Golemi D, Maveyraud L, Vakulenko SB, Zhang Y, Samama JP, Mobashery S. Molecular dynamics at the root of expansion of function in the M69L inhibitor-resistant TEM beta-lactamase from Escherichia coli. J Am Chem Soc. 2002 Aug 14;124(32):9422-30.

Vakulenko SB, Golemi D, Geryk B, Suvorov M, Knox JR, Mobashery S, Lerner SA. Mutational replacement of Leu-293 in the class C Enterobacter cloacae P99 beta-lactamase confers increased MIC of cefepime. Antimicrob Agents Chemother. 2002 Jun;46(6):1966-70.

Vakulenko S, Golemi D. Mutant TEM beta-lactamase producing resistance to ceftazidime, ampicillins, and beta-lactamase inhibitors. Antimicrob Agents Chemother. 2002 Mar;46(3):646-53.

Golemi D, Maveyraud L, Vakulenko S, Samama JP, Mobashery S. Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases. Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14280-5. Epub 2001 Nov 27.

Nagase T, Golemi D, Ishiwata A, Mobashery S. Inhibition of beta-lactamases by 6,6-bis(hydroxylmethyl)penicillanate. Bioorg Chem. 2001 Jun;29(3):140-5.

Golemi-Kotra D. and Mobashery S. Emergence of mechanisms of resistance in response to the challenge of antibiotics. Encyclopedia on-line, 2002.

Maveyraud L, Golemi D, Kotra LP, Tranier S, Vakulenko S, Mobashery S, Samama JP. Insights into class D beta-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa. Structure. 2000 Dec 15;8(12):1289-98.

Golemi D., Maveyraud L., Vakulenko S., Tranier S., Ishiwata A., Kotra LP., Samama JP., Mobashery S. The first structural and mechanistic insights for class D â-lactamases: Evidence for a novel catalytic process for turnover of β-lactam antibiotics. J. Am. Chem. Soc. 2000; 122(23): 6132-6133

Golemi D, Maveyraud L, Ishiwata A, Tranier S, Miyashita K, Nagase T, Massova I, Mourey L, Samama JP, Mobashery S. 6-(hydroxyalkyl)penicillanates as probes for mechanisms of beta-lactamases. J Antibiot (Tokyo). 2000;53(10):1022-7.

Kotra L. P., Golemi D., Amro N. A., Liu G. Y., Mobashery S. Dynamics of the lipopolysaccharide assembly on the surface of Escherichia coli. J. Am. Chem. Soc. 1999; 121(38):8707–8711

Swarén P, Golemi D, Cabantous S, Bulychev A, Maveyraud L, Mobashery S, Samama JP. X-ray structure of the Asn276Asp variant of the Escherichia coli TEM-1 beta-lactamase: direct observation of electrostatic modulation in resistance to inactivation by clavulanic acid. Biochemistry. 1999; 38(30):9570-6.