Article
Multidisciplinary Sciences
Son Tung Ngo, Khanh B. Vu, Minh Quan Pham, Nguyen Minh Tam, Phuong-Thao Tran
Summary: The winged-helix domain of wMUS81 is a potential cancer drug target that can be inhibited by marine fungi compounds through forming strong binding affinity. Eight compounds were identified as capable of preventing wMUS81 conformation by interacting with the enzyme via perturbation approach. The electrostatic interaction is the main factor in the binding process of ligands to wMUS81, with specific residues forming non-bonded contacts and hydrogen bonds with inhibitors.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Chemistry, Applied
Masoomeh Naseri, Ali Niazi, Kowsar Bagherzadeh, Elahe Konoz, Hamid Reza Samadikhah
Summary: An ultrasensitive electrochemical aptasensor based on modified glassy carbon electrode was developed to detect tetracycline in food samples. Molecular docking and molecular dynamic simulations were used to study the affinity and stability of antibiotics-aptamers complexes. The aptasensor, using kanamycin-specific aptamer, achieved a wide dynamic linear range and low limit of detection for tetracycline in milk samples.
Article
Materials Science, Paper & Wood
Antti Paajanen, Aleksi Rinta-Paavola, Jukka Vaari
Summary: This study investigates the thermal decomposition of cellulose using molecular simulations, revealing that depolymerization via glycosidic bond cleavage initiates the degradation process, leading to the formation of various oxygenates with water mainly formed in later stages. The reaction rate of glycosidic bond cleavage follows a sigmoidal model, providing insights into the mechanism of cellulose fast pyrolysis. The simulations, however, lack anhydrosugar forming reactions and thus offer limited understanding for industrial conditions.
Article
Biochemistry & Molecular Biology
Yasaman Mahmoodi, Faramarz Mehrnejad, Somayeh Khanmohammadi, Masoud Shahriari, Fereshteh Rahimi, Mohammad Reza Vakili, Afsaneh Lavasanifar
Summary: In this study, we investigated the influence of crystalline nanocellulose (CNC) on the structure and dynamics of human lysozyme (hLyz) using computational and spectroscopic methods. Our findings indicate that static quenching is the main mechanism for the formation of a stable CNC-hLyz complex, driven by electrostatic interactions. The structural elements and tertiary structure of the enzyme were mostly unaffected, except for the loop regions, in the presence of cellulose nanocrystals.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Carlos Alberto Lobato-Tapia, Yolotl Moreno-Hernandez, Zendy Evelyn Olivo-Vidal
Summary: Malaria remains a prominent disease in certain regions of Mexico, and compounds found in the Cecropia obtusifolia plant have shown potential as antimalarial drugs.
Article
Biochemistry & Molecular Biology
Tanusree Mookherjee, Angshuman Bagchi, Rita Ghosh
Summary: This study reveals a possible molecular mechanism of how the peptide circPPP1R12A can promote cancer by interfering with the Mst pathway. The peptide was found to bind to Mst1/2 proteins, preventing their interactions with Sav1 and inhibiting the activation of the Mst pathway.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Microbiology
Gustavo Marques Serra, Andrei Santos Siqueira, Fabio Alberto de Molfetta, Agenor Valadares Santos, Luciana Pereira Xavier
Summary: In this study, the beta-glucosidase from Microcystis aeruginosa CACIAM 03 (MaBgl3) was evaluated for its potential in cellulosic biomass bioconversion. The results showed that MaBgl3 is a stable enzyme with favorable binding free energy, making it suitable for cellulose hydrolysis.
Article
Biology
Jaikee Kumar Singh, Saumya Dubey, Gaurava Srivastava, Mohammad Imran Siddiqi, Sandeep Kumar Srivastava
Summary: COVID-19, caused by SARS-CoV-2, first emerged in Wuhan, China in December 2019. Since then, different variants of the virus have emerged. The recent emergence of the omicron variant and its sub-variants BA.1, BA.2, and BA.3 has shown a high infection rate and the ability to evade host immune defenses. In this study, the affinity of 80 drugs/compounds against omicron and its variants was evaluated using in silico docking calculations, and it was found that neohesperidin, a natural flavonoid, showed a stable interaction with the spike receptor domain of omicron and BA.2 compared to other variants. These findings could be important for developing specific therapeutic strategies against these novel variants.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Agriculture, Multidisciplinary
Jyoti Jaiswal, Amit Kumar Srivastav, Pradeep Kumar Rajput, Umesh C. S. Yadav, Umesh Kumar
Summary: This study aimed to improve the solubility and stability of cordycepin by encapsulating it in bovine serum albumin: beta-cyclodextrin nanoparticles. The synthesized nanoparticles showed sustained release of cordycepin and improved stability. In vitro studies also demonstrated greater cytotoxicity of the synthesized nanoparticles compared to free cordycepin.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Haritha Kalath, Abel John Koshy, Bhavya Banjan, Sowmya Soman, Gururaja Hosadevasthana, Rajesh Raju, Niyas Rehman, Amjesh Revikumar
Summary: This study investigated the active constituents in cabbage that interact with thyroid peroxidase (TPO) and their stability under cooking temperatures. The compound gamma-Terpinene was found to have the highest binding free energy, but it was susceptible to degradation at cooking temperature. Therefore, consuming cooked cabbage may be more beneficial for maintaining normal thyroid function.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Amgad Albohy, Eman Maher Zahran, Usama Ramadan Abdelmohsen, M. Alaraby Salem, Tarfah Al-Warhi, Mohammad M. Al-Sanea, Narek Abelyan, Hany Ezzat Khalil, Samar Yehia Desoukey, Mostafa Ahmed Fouad, Mohamed Salah Kamel
Summary: This article explores the potential of compounds derived from plants in combating the novel coronavirus. By analyzing the metabolomics and using chromatographic techniques, 14 compounds were identified and their binding interactions with viral targets were studied through molecular docking. The study reveals that three of these compounds have strong binding affinities and could potentially be used as antiviral drugs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Asaf Evrim Evren, Demokrat Nuha, Sam Dawbaa, Abdullah Burak Karaduman, Beguem Nurpelin Saglik, Leyla Yurttas
Summary: A new series of thiazole derivatives were synthesized and compounds 5a, 5b, and 5c showed promising anticancer activity against MCF7 cells, but not against A549 cells or L929 healthy cells. The acetamide moiety was found to play a pivotal role in the anticancer activity. Molecular docking and dynamics simulation studies revealed the binding modes and stability of the active compounds with the enzyme. The distance between the H-bond rich zone of the ligand and the heteroaryl ring system of the ligand was found to significantly impact the aromatase inhibitory activity.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Vasudevan Saranya, Ramachandran Radhika, Ramasamy Shankar, Subramaniam Vijayakumar
Summary: The study focuses on analyzing the complexes of E-protein with Papain, revealing the highest interaction value between E-protein (Glu76) and Papain (Cys25) complex. Molecular Dynamics simulation demonstrates that the E-protein (Ala54-Ile129) horizontal ellipsis Papain (Cys25) complex has the lowest root mean square deviation value compared to other complexes involving Papain (Asn175 & Hys159). The formation of a salt bridge between Asp103 and Lys110 residues is identified as an important stabilizing factor in the E-protein (Ala54-Ile129) horizontal ellipsis Papain (Cys25) complex.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
V. Sachithanandam, P. Lalitha, A. Parthiban, Jayaraman Muthukumaran, Monika Jain, Ranjita Misra, T. Mageswaran, R. Sridhar, R. Purvaja, R. Ramesh
Summary: The study reveals the potential of Quinizarin isolated from mangrove plants in exhibiting antimicrobial, antioxidant, and cytotoxic activities against certain bacteria and cancer cells.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Marzieh Dehghan Shasaltaneh, Elmira Naghdi, Zahra Moosavi-Nejad
Summary: This study investigates the interactions between RNase A and cCMP through molecular docking and molecular dynamics simulation. The results indicate that cCMP-RNase A complexes are stabilized through hydrophobic interaction, hydrogen bonding, and π-π stacking interaction. The enzyme-ligand docking study shows three phases of binding modes, and experimental methods confirm the activation and inhibition of substrate at different concentrations of cCMP.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Plant Sciences
Venu Gopal Vandavasi, Daniel K. Putnam, Qiu Zhang, Loukas Petridis, William T. Heller, B. Tracy Nixon, Candace H. Haigler, Udaya Kalluri, Leighton Coates, Paul Langan, Jeremy C. Smith, Jens Meiler, Hugh O'Neill
Article
Chemistry, Multidisciplinary
Oksana Gerlits, Troy Wymore, Amit Das, Chen-Hsiang Shen, Jerry M. Parks, Jeremy C. Smith, Kevin L. Weiss, David A. Keen, Matthew P. Blakeley, John M. Louis, Paul Langan, Irene T. Weber, Andrey Kovalevsky
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2016)
Meeting Abstract
Biophysics
Venu G. Vandavasi, Daniel K. Putnam, Qiu Zhang, Loukas Petridis, William T. Heller, B. Tracy Nixon, Candace H. Haigler, Udaya Kalluri, Leighton Coates, Paul Langan, Jeremy C. Smith, Jens Meiler, Hugh O'Neill
BIOPHYSICAL JOURNAL
(2016)
Article
Chemistry, Multidisciplinary
Daisuke Sawada, Yu Ogawa, Yoshiharu Nishiyama, Eiji Togawa, Satoshi Kimura, Paul Langan
CRYSTAL GROWTH & DESIGN
(2016)
Article
Chemistry, Physical
Richard J. Lindsay, Jan Siess, David P. Lohry, Trevor S. McGee, Jordan S. Ritchie, Quentin R. Johnson, Tongye Shen
JOURNAL OF CHEMICAL PHYSICS
(2018)
Article
Chemistry, Multidisciplinary
Quentin R. Johnson, Richard J. Lindsay, Tongye Shen
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Richard J. Lindsay, Bill Pham, Tongye Shen, Rachel Patton McCord
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Bill Pham, Richard J. Lindsay, Tongye Shen
Article
Chemistry, Medicinal
Bill Pham, Avery Bancroft Arons, Jeremy G. Vincent, Elias J. Fernandez, Tongye Shen
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2019)
Article
Biochemistry & Molecular Biology
Richard J. Lindsay, Rachael A. Mansbach, S. Gnanakaran, Tongye Shen
Summary: The conformational ensemble of intrinsically disordered proteins, such as α-synuclein, is crucial for understanding and preventing pathologies. Under low pH conditions, neutralization of negatively charged residues leads to compaction of the C-terminal portion of α-synuclein, while internal reorganization allows it to maintain its overall end-to-end distance.
BIOPHYSICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Priyojit Das, Tongye Shen, Rachel Patton McCord
Summary: Chromosome structures vary between different cell types and regions, and are influenced by factors such as epigenetic state.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Bill Pham, Ziju Cheng, Daniel Lopez, Richard J. Lindsay, David Foutch, Rily T. Majors, Tongye Shen
Summary: This study examines the receptor-ligand interaction patterns of the ROR gamma receptor and identifies key contacts essential to its constitutive activity. By analyzing crystal structures and performing computer simulations, the differences between agonist and inverse agonist binding are revealed. These findings have implications for the development of new drugs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
David Foutch, Bill Pham, Tongye Shen
Summary: Network analysis is a powerful tool for studying structural biology systems, with network centrality measurements and cluster coefficients helping identify key functional residues in proteins. Eigenvector centrality is sensitive in distinguishing structural features, while closeness centrality is less sensitive and more generic with respect to structural specificity. Modifications to protein structure networks (PSNs) can enhance sensitivity to discern structural changes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Priyojit Das, Tongye Shen, Rachel Patton McCord
BMC BIOINFORMATICS
(2020)
Article
Physics, Fluids & Plasmas
Priyojit Das, Rosela Golloshi, Rachel Patton McCord, Tongye Shen
