Dr. Rajni Verma, Ph.D. - Wichita State University - Lecturer

Dr. Rajni Verma

Ph.D.

Wichita State University

Lecturer

Wichita, Kansas | United States

Main Specialties: Chemistry

Additional Specialties: Computational Chemistry

ORCID logohttps://orcid.org/0000-0003-1247-0192


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Dr. Rajni Verma, Ph.D. - Wichita State University - Lecturer

Dr. Rajni Verma

Ph.D.

Introduction

Primary Affiliation: Wichita State University - Wichita, Kansas , United States

Specialties:

Additional Specialties:

Research Interests:

Education

Jul 2016
Wichita State University
Lecturer
Oct 2015
Washington University in St. Louis
Postdoc
Jul 2013
Wichita State University
Postdoc
Jan 2013
Jacobs University Bremen
Postdoc
Dec 2012
Jacobs University Bremen
Ph.D.

Experience

Jul 2017
Structure-dynamics of cofactor binding in human aldose reductases; Center of Biomedical Research Excellence in Protein Structure and Function, Kansas University, NIGMS, NIH
Co-PI
Apr 2017
Conformational dynamics and ligand binding in kynurenine 3-monooxygenase; Kansas IDeA Network of Biomedical Research Excellence, NIGMS, NIH
PI
Oct 2015 - Jun 2016
Washington University in Saint Louis
Postdoctoral Associate
Biomedical Engineering
Jul 2013 - Sep 2015
Wichita State University
Postdoctoral Associate
Department of Chemistry
Jul 2016
Wichita State University
Lecturer
Department of Chemistry

Publications

13Publications

103Reads

596Profile Views

17PubMed Central Citations

Progress in our understanding of 19F chemical shifts. Annual Reports on NMR Spectroscopy

Annual Reports on NMR Spectroscopy, 2017, 93, 281- 365

Annual Reports on NMR Spectroscopy

Fluorine NMR spectroscopy has diverse applications, including characterization of chemical reaction mechanisms, protein structure–function studies, and solid-state NMR characterization of crystalline, amorphous, and soft materials. Computational methods have aided in assigning and interpreting chemical shifts, with wide use in solid-state NMR spectroscopy. Work to understand fluorine chemical shifts has been aided by computational methods. So-called “normal” chemical shift behavior can be understood to arise from ground-state electron density, in which diamagnetic or Lamb shielding dominates. Meanwhile, electronic structure methods indicate that many instances of “reverse” chemical shift behavior can be understood to be dominated by paramagnetic shielding effects, which arise from the coupling of occupied and unoccupied molecular orbitals in the presence of a magnetic field. Calculations using natural chemical shielding analysis are used to delineate contributions from diamagnetic and paramagnetic shielding of fluorine nuclei in a set of aromatic molecules and aliphatic compounds, some of which exhibit reverse chemical shift behavior. An overview of recent advances to assign and interpret chemical shifts in complex environments is presented.

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August 2017
7 Reads

In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function

Catalysts 2017, 7(7), 212

Catalysts

Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme–substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.

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July 2017
7 Reads

To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent.

Mol Simul 2016;42(12):1001-1013. Epub 2016 Mar 22.

Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States.

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http://dx.doi.org/10.1080/08927022.2016.1139108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937824PMC
March 2016
15 Reads
3 Citations
1.133 Impact Factor

Unraveling Binding Effects of Cobalt(II) Sepulchrate with the Monooxygenase P450 BM-3 Heme Domain Using Molecular Dynamics Simulations.

J Chem Theory Comput 2016 Jan 17;12(1):353-63. Epub 2015 Dec 17.

School of Mathematics and Physics, University of Lincoln , Brayford Pool, Lincoln LN6 7TS, United Kingdom.

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http://dx.doi.org/10.1021/acs.jctc.5b00290DOI Listing
January 2016
15 Reads
1 Citation
5.500 Impact Factor

Molecular Modeling of Cetylpyridinium Bromide, a Cationic Surfactant, in Solutions and Micelle.

J Chem Theory Comput 2015 Nov 14;11(11):5415-25. Epub 2015 Oct 14.

Department of Chemistry, Wichita State University , McKinley Hall, 1845 Fairmount, Wichita, Kansas 67260-0051, United States.

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http://dx.doi.org/10.1021/acs.jctc.5b00475DOI Listing
November 2015
17 Reads
1 Citation
5.500 Impact Factor

The Mutagenesis Assistant Program.

Methods Mol Biol 2014 ;1179:279-90

Department of Chemistry, Wichita State University, Wichita, Kansas, USA.

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http://dx.doi.org/10.1007/978-1-4939-1053-3_19DOI Listing
March 2015
10 Reads
1 Citation

Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering.

Comput Struct Biotechnol J 2012 22;2:e201209008. Epub 2012 Oct 22.

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.

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http://dx.doi.org/10.5936/csbj.201209008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962222PMC
June 2014
7 Reads
4 Citations

Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations.

Biopolymers 2014 Mar;101(3):197-209

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany; Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany.

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http://dx.doi.org/10.1002/bip.22301DOI Listing
March 2014
9 Reads
3 Citations
2.385 Impact Factor

Conformational Dynamics of the FMN-Binding Reductase Domain of Monooxygenase P450BM-3.

J Chem Theory Comput 2013 Jan 20;9(1):96-105. Epub 2012 Dec 20.

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.

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http://dx.doi.org/10.1021/ct300723xDOI Listing
January 2013
9 Reads
2 Citations
5.500 Impact Factor

dRTP and dPTP a complementary nucleotide couple for the Sequence Saturation Mutagenesis (SeSaM) method

Journal of Molecular Catalysis B: Enzymatic

Methods to generate random mutant libraries in directed evolution are limited in functional diversity generation. The Sequence Saturation Mutagenesis (SeSaM) method was reported as a four step random mutagenesis method overcoming the limitations of epPCR based mutagenesis methods. SeSaM targets in contrast to epPCR each nucleotide “equally” avoiding mutagenic hot spots, achieving subsequent mutations in a codon (up to 37.1%), and allowing to adjust mutational biases through employed universal bases. In this manuscript, we report an advanced SeSaM method in which a protocol was developed and optimized for implementing the R (ribavirin) base in a SeSaM experiment. The R-based protocol was subsequently combined with the original P-base SeSaM protocol. Combining P- and R-base allows in SeSaM experiments to generate transversions at all four nucleotides of a given sequence with an unmatched chemical diversity. Following the later strategy, we developed a combined P- (at A & G positions) and R-base (at T & C positions) protocol, nearly doubled in comparison to the SeSaM-P [27] the number of mutations that are unobtainable by epPCR and removed the requirement of a single stranded template in the SeSaM method.

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December 2012
10 Reads

MAP(2.0)3D: a sequence/structure based server for protein engineering.

ACS Synth Biol 2012 Apr 22;1(4):139-50. Epub 2012 Feb 22.

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.

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http://dx.doi.org/10.1021/sb200019xDOI Listing
April 2012
9 Reads
1 Citation
3.951 Impact Factor

A potential antitumor drug (arginine deiminase) reengineered for efficient operation under physiological conditions.

Chembiochem 2010 Nov;11(16):2294-301

Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.

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http://dx.doi.org/10.1002/cbic.201000458DOI Listing
November 2010
12 Reads
1 Citation
3.090 Impact Factor

Followers

krishnaiah Damarla
krishnaiah Damarla

CSIR-CSMCRI