Article
Chemistry, Physical
A. Herlin Shamina, V. Bena Jothy
Summary: The optimal geometries and vibration spectra of Iminodiacetic Acid Hydrochloride (IAH) have been determined using density functional theory computations. The most stable structure of IAH was found through conformational analysis. Vibrational spectra were examined using potential energy distribution (PED) to interpret IR and Raman spectra both quantitatively and qualitatively. UV-Visible and NMR spectral studies of IAH were performed using both theoretical and experimental calculations. Chemical reactivity descriptors were computed to predict the reactivity and stability of the molecule. Mapping the charge density isosurface with electrostatic potential surface (ESP) revealed molecule size, shape, electrical potential distribution, and point of chemical reactivity. ELF and LOL maps depicted topological aspects of IAH. The hyperconjugative interactions causing the NLO activity and the hyper polarizability values suggest potential electro-optical applications. Moreover, IAH was screened for pharmacological activity, and its binding location to a target protein was predicted through molecular docking studies.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
C. Dabora Vincy, J. D. Deephlin Tarika, X. D. Divya Dexlin, A. Rathika, T. Joselin Beaula
Summary: Diaminoethane hexanedionic acid, selected for its antibacterial property, is extensively used for spectroscopic elucidations and computational aspects. Various methods have been applied to study its molecular structure, vibrational spectra assignments, nonlinear optical properties, electronic transitions, molecular reactivity, etc.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Chemistry, Physical
V. Gifty, V. Bena Jothy
Summary: NTA was used without purification and analyzed using density functional theory calculations. The study provided information on the molecular geometries, vibrational spectra, and docking analysis of NTA. The results showed the occurrence of charge transport within the molecule and the potential applications in electro optical fields. The antibacterial activity and drug likeness of NTA were also evaluated.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Infectious Diseases
Payal Gupta, Prasanta K. Dash, Tenkabailu Dharmanna Sanjay, Sharat Kumar Pradhan, Rohini Sreevathsa, Rhitu Rai
Summary: phlD is a novel polyketide synthase involved in the biosynthesis of phloroglucinol by condensing and cyclizing three molecules of malonyl-CoA. Phloroglucinol or DAPG is an important antibiotic produced by pseudomonads, which exhibits broad spectrum anti-bacterial and anti-fungal properties and triggers systemic resistance in plants. The cloning and analysis of the phlD gene from pseudomonads was reported, and a three-dimensional model for the PHLD protein was predicted. The study aimed at developing biopesticides for the biocontrol of rhizospheric pathogens.
Article
Biochemistry & Molecular Biology
Benjamin Tam, Siddharth Sinha, Zixin Qin, San Ming Wang
Summary: The TP53 gene plays a critical role in maintaining genome stability, but many of its variants remain unclassified due to lack of evidence. This study investigated the deleteriousness of missense variants in TP53 using a novel method, showing higher specificity in classification compared to other in silico methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Mourad Stitou, Hamid Toufik, Mohammed Bouachrine, Fatima Lamchouri
Summary: Using computational methods and bioinformatics techniques, potential inhibitors targeting the KRAS mutated protein were screened using various analytical and simulation methods, and the accuracy and stability of the simulation results were validated.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Soon Woo Park, Byung Ho Lee, Seung Hun Song, Moon Ki Kim
Summary: Ramachandran plots have been widely used in structural biology to describe protein structures. However, there is a limited number of data points in the Ramachandran plot and it cannot reflect protein steric information. In this study, we investigated protein secondary structure in terms of static and dynamic characteristics. The static analysis revealed a relationship between secondary structure proportion and residue hydrophobicity. The dynamic analysis using normal mode analysis showed high B-factors at the edge of the alpha helix region. Our findings provide valuable insight into protein structural studies.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Megha Kaviraj, Upendra Kumar, A. K. Nayak, Soumendranath Chatterjee
Summary: This study conducted in-silico protein modeling of NrfA in three model DNRA bacteria, revealing that the majority of NrfA protein is located in the periplasm and is hydrophilic. Conserved motifs and amino acid sequences were identified, and a novel identical sequence between serine and proline was discovered. Modeller was found to be the best tool for predicting NrfA protein. These findings contribute to the identification of unexplored DNRA bacteria and shed light on the N-retention processes.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Chemistry, Physical
Ushasi Pramanik, Anju Ajayan Kongasseri, Shashi Shekhar, Ashwin Mathew, Rahul Yadav, Saptarshi Mukherjee
Summary: The research discovered that Lysozyme interacts with Bisphenol S through static quenching, in which hydrophobic force plays a dominant role; tryptophan plays a crucial role in binding; the structural alteration in Lysozyme may affect its functional properties as a food preservative.
Article
Biochemistry & Molecular Biology
Amit Kumar Srivastav, Jyoti Jaiswal, Umesh Kumar
Summary: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) affects human respiratory function and causes COVID-19 disease. Screened from natural resources like edible mushrooms and marine fungi, bioactive compounds show strong potential to interact with SARS-CoV-2 and inhibit its enzymatic protease activity. However, these results are based on in silico studies and further clinical trials are needed for validation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Steven Hayward, E. James Milner-White
Summary: In amyloid diseases, insoluble amyloid fibrils are formed via a soluble oligomeric intermediate that mediates toxicity. The structure of this intermediate, potentially with an alpha-sheet structure, is controversial. Studies on peptide motifs like nests and alpha-strands show preferences for certain chain conformations, with glycine favoring gamma L and charged/polar amino acids favoring alpha L, which may impact alpha-sheet formation.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nicole Balasco, Luciana Esposito, Alfonso De Simone, Luigi Vitagliano
Summary: This study investigated the structural basis of conformational preferences of genetically encoded amino acid residues, revealing that different regions of the Ramachandran plot may exhibit similar or anticorrelated amino acid propensities.
Article
Chemistry, Physical
Zhili Lu, Qiaoxian Zhong, Jingxian Li, Bingjie Zhou, Yan-Ni Xing, Kaien Liu, Kexin Cao, Dongming Lan, Teng Zhou, Yonghua Wang, Jiaqi Wang
Summary: This study used computational approaches and mutagenesis strategies to enhance the stability of a diacylglycerol-specific lipase. Several mutations were found to significantly improve the thermostability and enzymatic activity of the enzyme. Structural analysis revealed how these mutations can release steric strain and increase stability. This suggests that substitution with glycine could be a promising strategy for improving protein thermostability.
Article
Biochemistry & Molecular Biology
Mayank Kumar, R. S. Rathore
Summary: The Ramachandran steric map is used to describe the conformation space of protein structures. This study focused on identifying disallowed spots in protein structures and found that certain residues tend to occur in disallowed conformations. Short loops and residues involved in interactions were particularly affected by conformational strain. Additionally, certain amino acids were found to have a higher tendency to occur in disallowed conformations.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2023)
Article
Biology
Nuzhat Bano, Shamim Akhtar Ansari, Abeer Hashem, Elsayed Fathi Abd Allah, Mohammad Israil Ansari
Summary: Teak, a valuable source of timber, showed partial amplification of the PMEI gene, which may enhance its tolerance to various stresses and adverse conditions.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2021)
