Search

Your search keyword '"Rajan, Rakhi"' showing total 50 results
Start Over Author "Rajan, Rakhi"
50 results on '"Rajan, Rakhi"'

1. idMotif: An Interactive Motif Identification in Protein Sequences

Author

Park, Ji Hwan, Prasad, Vikash, Newsom, Sydney, Najar, Fares, and Rajan, Rakhi

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Graphics, Computer Science - Human-Computer Interaction, Computer Science - Machine Learning
Abstract

This article introduces idMotif, a visual analytics framework designed to aid domain experts in the identification of motifs within protein sequences. Motifs, short sequences of amino acids, are critical for understanding the distinct functions of proteins. Identifying these motifs is pivotal for predicting diseases or infections. idMotif employs a deep learning-based method for the categorization of protein sequences, enabling the discovery of potential motif candidates within protein groups through local explanations of deep learning model decisions. It offers multiple interactive views for the analysis of protein clusters or groups and their sequences. A case study, complemented by expert feedback, illustrates idMotif's utility in facilitating the analysis and identification of protein sequences and motifs., Comment: IEEE CGA

Published
2024
Full Text
View/download PDF

13. Topoisomerases

Author

Rajan, Rakhi, Critchelow, Chandra, Mondragón, Alfonso, and Roberts, Gordon C. K., editor

Published
2013
Full Text
View/download PDF

34. Probing the catalytic mechanism of S-ribosylhomocysteinase (LuxS) with catalytic intermediates and substrate analogues

Author

Gopishetty, Bhaskar, Jinge Zhu, Rajan, Rakhi, Sobczak, Adam J., Wnuk, Stanislaw F., Bell, Charles E., and Dehua Pei

Subjects
Catalysis -- Analysis, Enzyme binding -- Analysis, Homocysteine -- Chemical properties, Ketones -- Chemical properties, Mutation (Biology) -- Analysis, Chemistry
Abstract

The 3-ketone intermediate is chemically prepared and is shown to be chemically and kinetically competent in the S-ribosylhomocysteinase (LuxS) catalytic pathway. The analysis of the kinetics of halide release and decay of the 3-ketone intermediate catalyzed by wild-type and mutant LuxS enzymes have disclosed that Cys-84 is the general base responsible for proton abstraction in the three reaction steps, whereas Glu-57 has facilitated substrate binding and proton transfer during catalysis.

Published
2009

36. Crystal structure of S-Ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate

Author

Rajan, Rakhi, Jinge Zhu, Xubo Hu, Dehua Pei, and Bell, Charles E.

Subjects
Binding sites (Biochemistry) -- Research, Ribosomal RNA -- Research, Ketones -- Chemical properties, Biological sciences, Chemistry
Abstract

S-Ribosylhomocysteinase (LuxS) is a Fe(super 2+) dependent metalloenzyme that catalyzes the cleavage of the thioether bond in S-Ribosylhomocysteinase (SRH) to produce homocysteine and 4,5-dihydroxy-2, 3-pentanedione (DPD), the precursor of type II bacterial quorum-sensing molecule. The study has provided direct evidence for the acid function of the metal ion in LuxS-catalyzed reaction and also reveals new insights into the catalytic function of active site residues.

Published
2005

41. Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs

Author

Chan, Clarence W., Badong, Deanna, Rajan, Rakhi, and Mondragón, Alfonso

Abstract

Ubiquitous across all domains of life, tRNAs constitute an essential component of cellular physiology, carry out an indispensable role in protein synthesis, and have been historically the subject of a wide range of biochemical and biophysical studies as prototypical folded RNA molecules. Although conformational flexibility is a well-established characteristic of tRNA structure, it is typically regarded as an adaptive property exhibited in response to an inducing event, such as the binding of a tRNA synthetase or the accommodation of an aminoacyl-tRNA into the ribosome. In this study, we present crystallographic data of a tRNA molecule to expand on this paradigm by showing that structural flexibility and plasticity are intrinsic properties of tRNAs, apparent even in the absence of other factors. Based on two closely related conformations observed within the same crystal, we posit that unbound tRNAs by themselves are flexible and dynamic molecules. Furthermore, we demonstrate that the formation of the T-loop conformation by the tRNA TΨC stem–loop, a well-characterized and classic RNA structural motif, is possible even in the absence of important interactions observed in fully folded tRNAs.

Published
2020
Full Text
View/download PDF

48. Structural and functional studies of the bacterial RECA protein

Author

Rajan, Rakhi

Subjects
Biophysics, General, Homologous recombination, RecA, double stranded DNA break, x-ray crystallography, LuxS
Abstract

RecA is the key player that mediates the DNA strand exchange reaction in the recombination process, which is essential for the repair of double stranded (ds) DNA breaks. The bacterium Deinococcus radiodurans (Dr) is extremely resistant to high doses of ionizing radiation because of its highly efficient capacity to repair dsDNA breaks. The Dr RecA protein promotes DNA strand-exchange by an unprecedented inverse pathway, in which the presynaptic filament is formed on dsDNA instead of ssDNA. In order to gain insight into the novel mechanistic features of Dr RecA protein, the x-ray crystal structure of Dr RecA was determined. Although the overall fold of Dr RecA is similar to E. coli RecA, there is a large reorientation of the C-terminal domain, which in E. coli RecA has a site for binding dsDNA. Compared to E. coli RecA, the inner surface along the central axis of the Dr RecA filament has an increased positive electrostatic potential. RecA generally binds to any sequence of ssDNA but has a preference for GT-rich sequences. The binding of RecA to DNA is phased relative to the GT sequences, with a periodicity of three nucleotides. A RecA coprotease assay was used to further probe the ssDNA sequence specificity of E. coli RecA protein. The coprotease activity of RecA is strongly dependent on the ssDNA sequence, with TGG-repeating sequences giving by far the highest coprotease activity. For selected trinucleotide-repeating sequences, the DNA-dependent ATPase and DNA-binding activities of RecA were also determined. The DNA-binding and coprotease activities of RecA have the same sequence dependence, which is essentially opposite to that of the ATPase activity of RecA. S-Ribosylhomocysteinase (LuxS) is the enzyme which catalyses the synthesis of the precursor of type II bacterial quorum sensing molecule (AI-2). AI-2 is very important in antibiotic development, since it mediates inter-species communication with in bacteria. A catalytically inactive mutant of Bacillus subtilis LuxS was co-crystallized with a 2-ketone intermediate. The structure reveals that the C2 carbonyl oxygen is directly coordinated with the metal ion, providing strong support for the proposed Lewis acid function of the metal ion during catalysis.

Published
2007

49. Helical transition of the bridge helix of Cas12a is an allosteric regulator of R-loop formation and RuvC activation.

Author

Ganguly C, Martin L, Aribam S, Thomas LM, and Rajan R

Abstract

CRISPR-Cas12a is widely used for genome editing and biomarker detection since it can create targeted double-stranded DNA breaks and promote non-specific DNA cleavage after identifying specific DNA. To mitigate the off-target DNA cleavage of Cas12a, we previously developed a Francisella novicida Cas12a variant (FnoCas12a KD2P ) by introducing double proline substitutions (K969P/D970P) in a conserved helix called the bridge helix (BH). In this work, we used cryogenic electron microscopy (cryoEM) to understand the molecular mechanisms of BH-mediated activation of Cas12a. We captured five structures of FnoCas12a KD2P at different states of conformational activation. Comparison with wild-type (FnoCas12a WT ) structures unravels a mechanism where BH acts as a trigger that allosterically activates REC lobe movements by tracking the number of base pairs in the growing RNA-DNA hybrid to undergo a loop-to-helical transition and bending to latch onto the hybrid. The transition of the BH is coupled to the previously reported loop-to-helix transition of the "lid", essential for opening RuvC endonuclease, through direct interactions of residues of the BH and the lid. We also observe structural details of cooperativity of BH and "helix-1" of RuvC for activation, a previously proposed interaction. Overall, our study enables development of high-fidelity Cas12a and Cas9 variants by BH-modifications.

Published
2025
Full Text
View/download PDF

50. Differential Divalent Metal Binding by SpyCas9's RuvC Active Site Contributes to Nonspecific DNA Cleavage.

Author

Newsom SN, Wang DS, Rostami S, Schuster I, Parameshwaran HP, Joseph YG, Qin PZ, Liu J, and Rajan R

Subjects
Catalytic Domain, CRISPR-Cas Systems genetics, RNA, Guide, CRISPR-Cas Systems, Endonucleases, Streptococcus pyogenes genetics, DNA Cleavage, Gene Editing
Abstract

To protect against mobile genetic elements (MGEs), some bacteria and archaea have clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) adaptive immune systems. CRISPR RNAs (crRNAs) bound to Cas nucleases hybridize to MGEs based on sequence complementarity to guide the nucleases to cleave the MGEs. This programmable DNA cleavage has been harnessed for gene editing. Safety concerns include off-target and guide RNA (gRNA)-free DNA cleavages, both of which are observed in the Cas nuclease commonly used for gene editing, Streptococcus pyogenes Cas9 (SpyCas9). We developed a SpyCas9 variant (SpyCas9 H982A ) devoid of gRNA-free DNA cleavage activity that is more selective for on-target cleavage. The H982A substitution in the metal-dependent RuvC active site reduces Mn 2+ -dependent gRNA-free DNA cleavage by ∼167-fold. Mechanistic molecular dynamics analysis shows that Mn 2+ , but not Mg 2+ , produces a gRNA-free DNA cleavage competent state that is disrupted by the H982A substitution. Our study demonstrates the feasibility of modulating cation:protein interactions to engineer safer gene editing tools.

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results