Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

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Recent Developments in Azole Compounds as Antitubercular Agent

Mini-Reviews in Organic Chemistry ◽

10.2174/1570193x15666180622144414 ◽

2019 ◽

Vol 16 (3) ◽

pp. 290-306

Author(s):

Rina Das ◽

Gyati S. Asthana ◽

Krishan A. Suri ◽

Dinesh Mehta ◽

Abhay Asthana

Keyword(s):

Therapeutic Agent ◽

Current Problem ◽

Noncovalent Interactions ◽

Drug Resistant ◽

Antitubercular Drugs ◽

Chemistry Research ◽

Improper Use ◽

Recent Developments ◽

Important Direction ◽

Tuberculosis Therapy

Tuberculosis (TB) is a global health disaster and is a wide-reaching hitch. The improper use of antibiotics in chemotherapy of TB patients led to the current problem of tuberculosis therapy which gives rise to Multi-Drug Resistant (MDR) strains. Nitrogen heterocycles including azole compounds are an important class of therapeutic agent with electron-rich property. Azole-based derivatives easily bind with the enzymes and receptors in organisms through noncovalent interactions, thereby possessing various applications in medicinal chemistry. Research on azoles derivatives have been expansively carried out and have become one of the extremely active area in recent years and the progress is quite rapid. A genuine attempt to review chemistry of azoles and to describe various azole-based compounds synthesized in the last two decades having promising antitubercular potential is described in the present article. It is hopeful that azole compounds may continue to serve as an important direction for the exploitation of azole-based antitubercular drugs with better curative effect, lower toxicity, less side effects, especially fewer resistances and so on.

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Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins

International Journal of Molecular Sciences ◽

10.3390/ijms22052647 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2647

Author(s):

M. Quadir Siddiqui ◽

Maulik D. Badmalia ◽

Trushar R. Patel

Keyword(s):

Nucleic Acid ◽

Nuclear Export ◽

Consensus Sequence ◽

Nuclear Export Signal ◽

Bioinformatic Analysis ◽

Nucleic Acid Binding ◽

Protein Protein Interaction ◽

Lim Domains ◽

Protein Nucleic Acid ◽

And Function

Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.

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Purification and functional characterization of adenovirus ts111A DNA-binding protein. Fluorescence studies of protein-nucleic acid binding.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)39444-x ◽

1990 ◽

Vol 265 (10) ◽

pp. 5875-5882

Author(s):

M L Meyers ◽

K M Keating ◽

W J Roberts ◽

K R Williams ◽

J W Chase ◽

...

Keyword(s):

Nucleic Acid ◽

Dna Binding ◽

Binding Protein ◽

Functional Characterization ◽

Dna Binding Protein ◽

Nucleic Acid Binding ◽

Protein Fluorescence ◽

Fluorescence Studies ◽

Protein Nucleic Acid

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Neutron Inelastic Scattering, Optical Spectroscopies and Scaled Quantum Mechanical Force Fields for Analyzing the Vibrational Dynamics of Pyrimidine Nucleic Acid Bases. 1. Uracil

The Journal of Physical Chemistry ◽

10.1021/jp952485x ◽

1996 ◽

Vol 100 (13) ◽

pp. 5224-5234 ◽

Cited By ~ 64

Author(s):

A. Aamouche ◽

M. Ghomi ◽

C. Coulombeau ◽

H. Jobic ◽

L. Grajcar ◽

...

Keyword(s):

Nucleic Acid ◽

Inelastic Scattering ◽

Force Fields ◽

Mechanical Force ◽

Quantum Mechanical ◽

Nucleic Acid Bases ◽

Vibrational Dynamics ◽

Neutron Inelastic Scattering ◽

Mechanical Force Fields

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Visible Light Photochemical Reactions for Nucleic Acid-Based Technologies

Molecules ◽

10.3390/molecules26030556 ◽

2021 ◽

Vol 26 (3) ◽

pp. 556

Author(s):

Bonwoo Koo ◽

Haneul Yoo ◽

Ho Jeong Choi ◽

Min Kim ◽

Cheoljae Kim ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Visible Light ◽

Chemical Reactions ◽

Chemical Biology ◽

Photochemical Reactions ◽

Reaction Conditions ◽

Promising Tool ◽

Recent Developments ◽

Visible Light Driven

The expanding scope of chemical reactions applied to nucleic acids has diversified the design of nucleic acid-based technologies that are essential to medicinal chemistry and chemical biology. Among chemical reactions, visible light photochemical reaction is considered a promising tool that can be used for the manipulations of nucleic acids owing to its advantages, such as mild reaction conditions and ease of the reaction process. Of late, inspired by the development of visible light-absorbing molecules and photocatalysts, visible light-driven photochemical reactions have been used to conduct various molecular manipulations, such as the cleavage or ligation of nucleic acids and other molecules as well as the synthesis of functional molecules. In this review, we describe the recent developments (from 2010) in visible light photochemical reactions involving nucleic acids and their applications in the design of nucleic acid-based technologies including DNA photocleaving, DNA photoligation, nucleic acid sensors, the release of functional molecules, and DNA-encoded libraries.

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