Article
Multidisciplinary Sciences
Seyed Arad Moghadasi, Emmanuel Heilmann, Ahmed Magdy Khalil, Christina Nnabuife, Fiona L. Kearns, Chengjin Ye, Sofia N. Moraes, Francesco Costacurta, Morgan A. Esler, Hideki Aihara, Dorothee von Laer, Luis Martinez-Sobrido, Timothy Palzkill, Rommie E. Amaro, Reuben S. Harris
Summary: Vaccines and drugs have been effective in reducing disease severity and slowing down the spread of SARS-CoV-2. However, the continuous transmission and evolution of the virus can lead to the emergence of variants resistant to these interventions. This study investigates the resistance of natural variants of the main protease of SARS-CoV-2 to protease inhibitors. The findings show that certain variants are resistant to specific inhibitors and have existed before the introduction of these drugs. It is important to monitor resistant variants and develop new antiviral drugs for combination therapy.
Article
Biochemistry & Molecular Biology
Lucianna H. Santos, Ernesto R. Caffarena, Rafaela S. Ferreira
Summary: This study investigates the impact of non-covalent binding on the residues of the active site of the Zika virus NS2B/NS3 protease using theoretical computational methods. It is found that the protonation of catalytic residues can occur under different conditions, and non-covalent binding can affect the configuration of the active site.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biology
Mehdi Yoosefian, Maryam Zeraati Moghani, Alfredo Juan
Summary: Researchers have discovered a new human immunodeficiency virus (HIV) protease inhibitor called ATV7 through molecular docking and molecular dynamics simulation, which has better antiviral effects and inhibitory ability than the existing drug atazanavir.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Multidisciplinary Sciences
Ruiming Zhao, Hui Dai, Rodolfo J. Arias, Gerardo A. De Blas, Gerardo Orta, Martin A. Pavarotti, Rong Shen, Eduardo Perozo, Luis S. Mayorga, Alberto Darszon, Steve A. N. Goldstein
Summary: This study reveals the mechanism of albumin activation of hHv1 channels, enhancing open probability and proton current by binding to the channel voltage sensor domains. Alb activation is crucial for triggering sperm fertilization and sustaining immune inflammatory responses in neutrophils.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Sophie Roy, Niklaus Johner, Viktor Trendafilov, Ivan Gautschi, Olivier Bignucolo, Ophelie Molton, Simon Berneche, Stephan Kellenberger
Summary: The extracellular Ca2+ concentration affects the function of ion channels in the nervous system, and we investigated how Ca2+ controls the activity of ASIC3. We discovered a new regulatory site in ASIC3 and demonstrated that ASIC3 activation involves the unbinding of Ca2+ from the channel pore.
Article
Biotechnology & Applied Microbiology
Fabian Falkenberg, Leonie Voss, Michael Bott, Johannes Bongaerts, Petra Siegert
Summary: The aim of this study was to characterize four new subtilisins from halotolerant and halophilic microorganisms. The proteases showed activity over a wide pH range and exhibited high stability towards SDS and high concentrations of NaCl. These enzymes demonstrate potential for future biotechnological applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Zongchao Chen, Pengfei Niu, Xiaomei Ren, Wenlong Han, Ruyu Shen, Min Zhu, Yang Yu, Chan Ding, Shengqing Yu
Summary: Recent studies have shown that the secreted subtilisin-like serine protease SspA in Riemerella anatipestifer is associated with bacterial virulence, proteolysis, and functions as an effector protein of the T9SS system, playing a crucial role in pathogenesis and host evasion.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Physics, Multidisciplinary
Tine Curk, Erik Luijten
Summary: Nanoparticles in solution acquire charge through surface groups, requiring the use of charge-regulating boundary conditions for proper description of electrostatic interactions. A hybrid Monte Carlo/molecular dynamics scheme is implemented to dynamically adjust charges of surface groups, qualitatively changing self-assembled structures. The conventional constant-charge approximation may be used under certain conditions, and the interplay between charge regulation and dielectric polarization is clarified.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Shashi Kumar, Parag A. Deshpande
Summary: This study investigates the thermodynamic stability of SazCA protein through molecular dynamics simulations in a temperature range of 293-393 K, revealing that the protein exhibits the highest structural stability at 353 K with increased flexibility at temperatures above. Analyses indicate that conformations at 353 K demonstrate the highest thermal stability and folding capacity, supporting a transition in folding/unfolding pathway at this temperature.
Article
Biochemistry & Molecular Biology
Harutyun Sahakyan, Karen Nazaryan, Arcady Mushegian, Irina Sorokina
Summary: Molecular dynamics simulations were performed to study protein folding. By applying rotational force to the C-terminal amino acid while restricting the movement of the N-terminal amino acid, the folding of four protein domains was accelerated at least by an order of magnitude. These results suggest that external forces and constraints can bias the motions of the polypeptide and facilitate the attainment of stable fold.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Soumil Y. Joshi, Samrendra Singh, Karteek K. Bejagam, Sanket A. Deshmukh
Summary: Research indicates that the self-folding of PNIPAM-grafted graphene is initiated by the weakening of PNIPAM-water interactions at higher temperatures, leading to strong hydrophobic interactions between graphene and PNIPAM. Coarse-grained molecular dynamics simulations provide important molecular-level insights for controlling and tuning the process of graphene self-folding.
Article
Agriculture, Multidisciplinary
Fenghua Wang, Xiangyang Ma, Ying Sun, Enping Guo, Chaoshuo Shi, Zhaoting Yuan, Yu Li, Qinggang Li, Fuping Lu, Yihan Liu
Summary: In this study, a tailored combination of loop engineering strategy and iterative saturation mutagenesis method was used to improve the activity of a protease from Bacillus clausii under cold conditions. An engineered variant called MT6 exhibited 18.3-fold higher catalytic efficiency than the wild-type variant at 10°C. Molecular dynamics simulations and dynamic tunnel analysis revealed that the introduced mutations increased the substrate-binding pocket volume and enhanced interactions with the substrate, leading to improved catalysis. This research provides insights and strategies for improving protease activity and offers a novel protease with enhanced activity under cold conditions for the food industry.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Ghadir A. Jamal, Ehsan Jahangirian, Michael R. Hamblin, Masoud Shirali, Hamed Mirzaei, Hossein Tarrahimofrad
Summary: The purpose of this study was to identify a thermostable protease from a thermophilic bacterium, Geobacillus stearothermophilus, named Protease JJ. Structural prediction and molecular dynamics simulations revealed that Protease JJ exhibited good structural and thermal stability, and it showed strong interactions with BSA and β-casein. The findings suggest that Protease JJ has potential as a thermostable protease for further research.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Panisak Boonamnaj, R. B. Pandey, Pornthep Sompornpisut
Summary: This study used molecular dynamics simulations to investigate the structural stability of the SARS-CoV-2 M-pro enzyme dimer at neutral and acidic pH. The results showed that the protein undergoes larger structural changes at acidic pH, indicating instability and a tendency for dimer dissociation. The loss of interaction energy in the dimer is mainly driven by electrostatic interactions. This research provides insights for rational drug design and target evaluation against COVID-19.
BIOPHYSICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Monikaben Padariya, Maciej Baginski, Minofar Babak, Umesh Kalathiya
Summary: The study found that the presence of Darunavir in different organic solvents can enhance protein-protein interactions within the protease homodimer, with the urea aqueous solution providing the highest stability. In systems with ethylene glycol or glycerol solvents, the flap domains of the enzyme formed an open conformation, leading to weak binding affinity with the drug.
BIOPHYSICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Shruti Koulgi, Vinod Jani, Mallikarjunachari Uppuladinne, Uddhavesh Sonavane, Asheet Kumar Nath, Hemant Darbari, Rajendra Joshi
Summary: The COVID-19 pandemic caused numerous deaths worldwide, with the causative agent being SARS-CoV-2 and its main protease as a key therapeutic target. Drug repurposing may be effective in targeting this virus, and simulation and structural analysis can help in identifying relevant drug molecules for binding to the main protease of SARS-CoV-2.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Shruti Koulgi, Vinod Jani, Vinay Nair, Jagmohan S. Saini, Samiron Phukan, Uddhavesh Sonavane, Rajendra Joshi, Raj Kamboj, Venkata Palle
Summary: Evaluation of cardiotoxicity potential of new chemical entities has become a stringent filter in drug discovery, with a focus on hERG channel protein inhibition. A computational model for the active-state of hERG was developed and showed noticeable conformational changes in the protein upon ligand-binding, potentially leading to a collapse of the pore and transition of hERG from an open to an inactive state. These findings could aid in designing compounds devoid of hERG inhibition and reduced cardiotoxicity.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Raghava R. Sunkara, Shrutiqs Koulgi, Vinod Jani, Nikhil Gadewal, Uddhavesh Sonavane, Rajendra Joshi, Sanjeev K. Waghmare
Summary: The cWnt signaling pathway plays a crucial role in stem cell maintenance and tissue homeostasis. SFRP1, a Wnt inhibitor, binds to Wnt ligands and frizzled receptors through different domains with varying affinities. SFRP1Netrin shows higher affinity for FZ receptors, potentially inhibiting the non-canonical Wnt-signaling pathway.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Shruti Koulgi, Vinod Jani, Mallikarjunachari V. N. Uppuladinne, Uddhavesh Sonavane, Rajendra Joshi
Summary: The study investigates the structural variations of RdRP and its binding with nucleotide analogues, where certain residues were found to have significant interactions with the ligands, potentially aiding in the design of new inhibitors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Mokshada Varma, Bhupendra Shravage, Sakharam Tayade, Avinash Kumbhar, Ray Butcher, Vinod Jani, Uddhavesh Sonavane, Rajendra Joshi, Prasad P. Kulkarni
Summary: Alzheimer's disease is a complex brain disorder involving multiple pathophysiological events, and targeting multiple mechanisms is necessary for its treatment. A novel methyl-substituted 3-acetylcoumarin thiosemicarbazone derivative shows potential in protecting against acetylcholinesterase activity, inflammation, and autophagy induction, as demonstrated in various cellular and animal models. The compound's molecular structure allows for better inhibition of AChE activity and peptide aggregation, suggesting promising therapeutic effects for AD.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Multidisciplinary Sciences
Shruti Koulgi, Vinod Jani, Mallikarjunachari V. N. Uppuladinne, Uddhavesh Sonavane, Rajendra Joshi
Summary: Drug repurposing studies targeting inhibition of RdRP of SARS-CoV-2 have shown the potential effect of small molecules. In this study, phytochemicals from Indian medicinal plants were found to have strong binding to RdRP, with cordifolide A and sitoindoside IX exhibiting high stability in binding.
Article
Biochemistry & Molecular Biology
Jingpeng Ge, Johannes Elferich, Sepehr Dehghani-Ghahnaviyeh, Zhiyu Zhao, Marc Meadows, Henrique von Gersdorff, Emad Tajkhorshid, Eric Gouaux
Summary: This study demonstrates how prestin in outer hair cells mediates signal amplification by coupling conformational changes to alterations in membrane surface area. Cryo-EM structures and computational studies reveal the allosteric coupling between the anion site and changes in the transmembrane domain and surrounding membrane. These findings provide insight into the electromotility of outer hair cells.
Article
Biology
E. P. Ramakrishnan, Saurabh Gupta, Renu Gadhari, Neeraj Bharti, Sandeep Malviya, Sunitha Manjari Kasibhatla, Jan Kim, Rajendra Joshi
Summary: GAMUT is a big data-based tool for efficient comparison of SNPs in different population samples, supporting dynamic querying and various charting options, with the ability to download data results for further analysis.
JOURNAL OF BIOSCIENCES
(2021)
Article
Biochemical Research Methods
Mallikarjunachari V. N. Uppuladinne, Dikshita Dowerah, Uddhavesh B. Sonavane, Suvendra Kumar Ray, Ramesh C. Deka, Rajendra R. Joshi
Summary: Five novel LNA-based antisense modifications were proposed and their properties were explored using computational methods, confirming their higher reactivity. Molecular dynamics simulations revealed that incorporation of A2 modification into RNA-RNA duplexes increased duplex binding affinity similar to LNA, while A3 modification showed lower binding compared to LNA but improved compared to MOE.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Anthropology
Manjari Jonnalagadda, Neeraj Bharti, Sunitha Manjari Kasibhatla, Mayur A. Wagh, Rajendra Joshi, Shantanu Ozarkar, Richa Ashma
Summary: The study analyzed the MC1R gene in West Maharashtra, India to investigate if sequence diversity corresponds to the diverse pigmentary profiles in different populations. The results showed that there was no evidence of selective constraint on MC1R and the MC1R polymorphisms may not be influencing pigmentation variation among castes and tribes in this region.
AMERICAN JOURNAL OF HUMAN BIOLOGY
(2022)
Article
Neurosciences
Jeffrey R. Holt, Melanie Tobin, Johannes Elferich, Eric Gouaux, Angela Ballesteros, Zhiqiang Yan, Zubair M. Ahmed, Teresa Nicolson
Summary: This review discusses the identification of components in the mechanosensory transduction complex in hair cells and the ongoing research interest in this area. Emerging evidence has implicated multiple molecular components in the transduction machinery, but the exact mechanism of how these components interact to enable hearing and balance remains unclear. The review aims to provide a deeper understanding of these components and highlight both areas of consensus and controversy, as well as opportunities for future scientific discovery in this field.
JARO-JOURNAL OF THE ASSOCIATION FOR RESEARCH IN OTOLARYNGOLOGY
(2021)
Article
Chemistry, Medicinal
Shruti Koulgi, Archana Achalere, Uddhavesh Sonavane, Rajendra Joshi
Summary: This study investigated the conformational variations of p53 at different temperatures using molecular dynamics simulations and Markov State Modeling analysis. The results revealed that p53 exhibits reduced functionality and weakened DNA binding ability at physiological temperatures. Potential target regions to overcome this temperature sensitivity were also identified.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Genetics & Heredity
Muthukumar Balamurugan, Ruma Banerjee, Sunitha Manjari Kasibhatla, Archana Achalere, Rajendra Joshi
Summary: This study analyzed core-cluster-specific single nucleotide polymorphisms (SNPs) of Mycobacterium tuberculosis var. africanum to determine its lineage and clustering patterns. The results identified two lineages, L5 and L6, with further sub-lineages within each lineage. The analysis of SNPs also revealed genetic variations associated with strain specificity and growth attenuation.
FRONTIERS IN GENETICS
(2022)
Article
Chemistry, Multidisciplinary
Shruti Koulgi, Vinod Jani, Samiron Phukan, Uddhavesh Sonavane, Rajendra Joshi, Rajender Kumar Kamboj, Venkata Palle
Summary: This study investigates the homotropic cooperativity of CYP3A4 inhibitor Ketoconazole (KLN) and the plasticity of the active site upon binding to different drug chemotypes using molecular dynamic simulation studies and structural analysis. The results demonstrate that binding of KLN at the heme binding site is energetically more stable, and involvement of hydrophobic residues increases during the homotropic cooperativity of ligands. The 3D volume occupancy of ligands determines the phenomenon of homotropic versus non-homotropic effect, as observed from the binding mode analysis of KLN (homotropic ligand) and Ritonavir (non-homotropic ligand).
Article
Biology
Johannes Elferich, Giulia Schiroli, David T. Scadden, Nikolaus Grigorieff, Edward H. Egelman
Summary: Localization of biomolecules inside a cell is a major goal of biological imaging. Fluorescence microscopy can localize biomolecules, but its accuracy is limited by visible light. Cryo-electron microscopy provides accurate position and orientation information, but is limited to small fields of view. In this study, a new data acquisition scheme called DeCo-LACE is used to collect high-resolution images of whole sections of neutrophil-like mouse cells, allowing for a better understanding of protein distribution.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)