Article
Agriculture, Multidisciplinary
Kaiwen Duan, Xiaofeng Ban, Yinglan Wang, Caiming Li, Zhengbiao Gu, Zhaofeng Li
Summary: This study investigated the effect of removing the carbohydrate-binding module (CBM) on the catalytic performance of the maltotetraose-forming amylase from Pseudomonas saccharophila. The results showed that while the removal of CBM slightly reduced the thermal stability and catalytic ability for long-chain substrates, it improved the catalytic ability and product specificity for substrates with shorter chain lengths. The mutant enzyme also exhibited higher G4 content and proportion compared to the wild-type enzyme.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Yanmei Hu, Huanan Li, Qiuping Ran, Jiashu Liu, Shanna Zhou, Qiming Qiao, Huiting Song, Fang Peng, Zhengbing Jiang
Summary: This study systematically explored the influence of CBM on the properties of GH6 exoglucanase, indicating that the binding ability of CBM is not necessary for the catalysis of CtCBH.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Materials Science, Multidisciplinary
Hilal Kivrak, Omer Faruk Er, Omruye Ozok, Sebahattin Celik, Arif Kivrak
Summary: A chemical antibody based on MPBB was developed for more effective detection of CA125 levels through electrochemical methods. The study found optimal conditions for MPBB loading, antigen concentration, and incubation time, as well as determined the linear ranges and detection limits of the electrode. Molecular docking results suggested MPBB as a promising alternative to marketed CA125 immunoassays.
MATERIALS CHEMISTRY AND PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Xin Ni, Tong Fu, Xueyan Wang, Jingjing Zhao, Zhimin Yu, Xianzhen Li, Fan Yang
Summary: Due to low accessibility of enzymes to xanthan substrates, enzymolysis of xanthan is deficient, hindering industrial production of functional oligoxanthan. This study investigated the role of two carbohydrate binding modules, MiCBMx and PspCBM84, in catalytic properties of endotype xanthanase MiXen. Results showed that PspCBM84 significantly increased thermostability, substrate affinity, and catalytic efficiency of endotype xanthanase. Presence of both CBMs enabled production of more oligoxanthan with higher antioxidant activity. These findings lay a foundation for rational design of endotype xanthanase and industrial production of oligoxanthan.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Leilei Liang, Qingchuan Zheng
Summary: alpha-TOH is a potent antioxidant that is closely related to human health. The metabolism of CYP4F2 plays a crucial role in regulating the concentrations of alpha-TOH. Through simulation experiments and mutation simulations, the key interactions between CYP4F2 and alpha-TOH were investigated, providing insights into the regulatory mechanism of CYP4F2 on the metabolism of alpha-TOH.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Avinash Kumar, Vinay Kumar Singh, Arvind M. Kayastha
Summary: This study determined the three-dimensional structure of fenugreek α-amylase using homology modeling and analyzed its molecular basis and mode of action through molecular dynamics simulations and molecular docking. The study identified functional groupings and binding interactions between the enzyme and its substrate maltose. The research provides valuable insights into the atomic-level molecular underpinnings of α-amylase interaction with maltose.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Cell Biology
Tanveer A. A. Wani, Seema Zargar
Summary: One of the top priorities in medicinal chemistry is the discovery of new molecules that have potential as anticancer agents. Compounds that interact with DNA, such as groove binders, alkylators, and intercalators, have shown promise as chemotherapeutic drugs for cancer treatment. This study focused on the anticancer drug 1,3,5-Tris(4-carboxyphenyl)benzene (H3BTB), which binds to DNA through groove binding and has demonstrated significant cytotoxic potential against breast and cervical cancer cell lines. Computational studies, including molecular docking and molecular dynamics simulations, supported the minor groove binding of H3BTB-DNA complex. This research will contribute to further empirical investigation into the synthesis of metallic and non-metallic derivatives of H3BTB and their potential as bioactive molecules for cancer treatment.
Article
Biochemistry & Molecular Biology
Murugesan Sankarganesh, Rajadurai Vijay Solomon, Jeyaraj Dhaveethu Raja
Summary: A new monometallic platinum complex was successfully synthesized and characterized by various techniques; structural and property studies were conducted through experiments and calculations; the research findings demonstrate the superior performance of the platinum complex in areas such as anticancer, antioxidant, and antimicrobial activities.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Preeti Jha, Shubhra Chaturvedi, Ruchika Bhat, Nidhi Jain, Anil K. Mishra
Summary: The 5HT1A receptor is crucial in the treatment of depression and anxiety disorders, and the developed homology model shows promise in designing high-affinity probes for these neurological disorders.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Chemistry, Multidisciplinary
Serge Perez, Olga Makshakova
Summary: Glycoscience encompasses the study of molecules and macromolecules containing carbohydrates, with computational methods ranging from quantum chemistry to molecular dynamics addressing their structural and dynamical features. The field covers a wide range of molecules in terms of quantity and occurrence, with the selection of computational methods depending on stereoelectronic effects from different aspects such as quantum chemistry to molecular dynamics and mechanics.
Article
Multidisciplinary Sciences
Markus Hackl, Edward V. Contrada, Jonathan E. Ash, Atharv Kulkarni, Jinho Yoon, Hyeon-Yeol Cho, Ki-Bum Lee, John M. Yarbrough, Cesar A. Lopez, Sandrasegaram Gnanakaran, Shishir P. S. Chundawat
Summary: Protein adsorption to solid carbohydrate interfaces is crucial in biological processes such as biomass deconstruction. This study focuses on understanding the interactions between carbohydrate-binding modules (CBMs) and polysaccharides to improve enzymatic efficiency in biomass deconstruction. The research presents a method using single-molecule force spectroscopy to study the unbinding behavior of CBMs from polysaccharide surfaces. The results reveal distinct CBM binding conformations and provide insights into the structural mechanisms through molecular dynamics simulations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biotechnology & Applied Microbiology
Jane Wittrup Agger, Michael Schmidt Madsen, Line Korte Martinsen, Pedro Alves Martins, Kristian Barrett, Anne S. Meyer
Summary: This review summarizes the latest research on glucuronoyl esterases (GEs), with a focus on fungal variants. The study reveals that fungal enzymes largely fall into one major branch, with only a minor subset of bacterial enzymes in the same branch. Additionally, some fungal proteins carry a CBM1 binding domain. Molecular docking experiments suggest that there are no direct interactions between the enzyme and lignin polymer, and an elongated carbon chain between the ester linkage and the first phenyl of lignin is preferred. The next step for these enzymes is to explore their application in utilizing lignocellulose as a renewable resource.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ardhendu Mandal, Abhijeet Thakur, Arun Goyal
Summary: This study investigated the biochemical properties of a recombinant 8-1,4 endoglucanase, AtGH9C-CBM3A-CBM3B, and the role of its associated CBMs in catalysis. The enzyme showed maximum activity at 55°C and pH 7.5, and exhibited high activity against carboxy methyl cellulose, lichenan, 8-glucan, and hydroxy ethyl cellulose. The catalytic module, AtGH9C, showed insignificant activity, emphasizing the essential requirement of CBMs in catalysis. The associated CBMs also contributed to thermostability. The results highlight the importance of the physical association and cross-talk between AtGH9C and its associated CBMs in efficient cellulose catalysis.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Physical
Mariana Barbosa, Helvio Simoes, Duarte Miguel E. Prazere
Summary: Functionalization of cellulose with biomolecules can lead to materials with enhanced properties, with the ability to control biological interactions. By efficiently combining relevant biomolecules into cellulose materials, novel functionalities can be achieved, paving the way for advanced medical diagnostic sensors or specialized biomaterials.
Article
Chemistry, Physical
Khlood Abou-Melha
Summary: In this study, acenaphthenequinone-thiosemicarbazone was utilized as a precursor for synthesizing various compounds including thiazolyl-pyrazoles. The structures of the synthesized compounds were elucidated through elemental analysis and spectral analysis. Both theoretical and experimental studies indicated good correlation with the anticancer activities of the synthesized derivatives.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Henrique S. Fernandes, Sergio F. Sousa, Nuno M. F. S. A. Cerqueira
Summary: This study utilized advanced computational methods to investigate the catalytic mechanism of SARS-CoV-2 M-pro, providing insights for the design of new antiviral drugs.
MOLECULAR DIVERSITY
(2022)
Article
Biochemistry & Molecular Biology
Andre F. Pina, Sergio F. Sousa, Nuno M. F. S. A. Cerqueira
Summary: The enzyme Pdx2 uses a Cys-His-Glu catalytic triad to convert glutamine into glutamate and ammonia, which is essential for the biosynthesis of PLP in pathogens causing Malaria and Tuberculosis. The catalytic mechanism involves six steps, with the hydrolytic step being the rate-limiting one. This unique catalytic mechanism of Pdx2 presents opportunities for developing new inhibitors to target the enzyme and combat diseases like Malaria and Tuberculosis.
Article
Chemistry, Physical
Rui P. P. Neves, Ana Cunha, Pedro A. Fernandes, Maria J. Ramos
Summary: In this study, QM/MM molecular dynamics simulations were used to investigate the rate-limiting step of the glycosylation reaction of pancreatic alpha-amylase. By carefully selecting different starting conformations and performing umbrella sampling simulations, Gibbs energy profiles were calculated. The results showed that the starting conformation has a significant impact on the reaction energy and activation energy.
Article
Chemistry, Multidisciplinary
Pedro A. Fernandes, Oscar Passos, Maria J. Ramos
Summary: The COVID-19 pandemic has posed challenges to teaching, and this article proposes the use of modern technology to create a virtual classroom for hands-on molecular bioinformatics courses, allowing students to learn effectively despite the lockdowns. The outcomes of this virtual classroom are comparable to the traditional teaching method.
JOURNAL OF CHEMICAL EDUCATION
(2022)
Article
Agriculture, Multidisciplinary
Barbara Torres-Rochera, Elvira Manjon, Natercia F. Bras, Maria Teresa Escribano-Bailon, Ignacio Garcia-Estevez
Summary: This study investigates the supramolecular interactions between the major wine anthocyanin, malvidin-3-O-glucoside, and different wine phenolic compounds under acidic conditions. The color variations of the anthocyanin are evaluated, and the interaction constants with the phenolic compounds are determined. Hydrophobic interactions and hydrogen bonds play important roles in the pigment/copigment aggregation, while hydrophobic interactions are more significant when caffeic acid is involved.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Juliana Castro-Amorim, Ana Oliveira, Ashis K. Mukherjee, Maria J. Ramos, Pedro A. Fernandes
Summary: In this study, the catalytic mechanism of RVV-X was determined using a density functional theory/molecular mechanics approach. The results showed that the catalytic process occurs in two steps, involving nucleophilic attack and protonation of the substrate. Zn2+ was found to play a unique role in catalysis by lowering the pKa of the Zn2+-bound water molecule.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Juliana Castro-Amorim, Ana Novo de Oliveira, Saulo Luis Da Silva, Andreimar M. Soares, Ashis K. Mukherjee, Maria Joao Ramos, Pedro A. . Fernandes
Summary: Snake venom-secreted phospholipase A(2) (svPLA(2)) enzymes play a crucial role in envenoming by disrupting the cell membrane's integrity and inducing various pharmacological effects. However, the reaction mechanisms of svPLA(2) are still not fully understood. This review presents and analyzes the most plausible reaction mechanisms, including the single-water mechanism and the assisted-water mechanism. The importance of interfacial activation and a potential catalytic mechanism for noncatalytic PLA(2)-like proteins are also discussed.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Joao P. M. De Sousa, Nuno C. S. A. Oliveira, Pedro A. Fernandes
Summary: (S)-Norcoclaurine is a crucial compound for the biosynthesis of benzylisoquinoline alkaloids, including various drugs. The genetic modification of (S)-norcoclaurine synthase has been proven to be an effective strategy for large-scale bioproduction of (S)-norcoclaurine in heterologous hosts such as bacteria or yeast.
Article
Chemistry, Physical
Rui P. P. Neves, Bruno Araujo, Maria J. Ramos, Pedro A. Fernandes
Summary: The bacterium Rhodococcus erythropolis (strain IGTS8) has a significant potential in the industry for its ability to remove sulfur from crude oil through the 4S metabolic pathway. The rate-limiting enzyme DszC is prone to feedback inhibition. Molecular docking and dynamics simulations were used to identify binding sites wherein two products of the pathway induce feedback inhibition. The study revealed four potential binding sites, and the proposed mechanism of feedback inhibition involves disturbance of oligomerization and weakening of key interactions within DszC.
Article
Pharmacology & Pharmacy
Carlos F. M. Silva, Teresa Leao, Filipa Dias, Ana M. Tomas, Diana C. G. A. Pinto, Eduardo F. T. Oliveira, Ana Oliveira, Pedro A. Fernandes, Artur M. S. Silva
Summary: Leishmaniasis is a neglected disease mainly affecting people in developing countries, with approximately 350 million people at risk. The lack of vaccines and chemotherapy has led to an increase in the incidence of the disease. A computational study focusing on a specific enzyme of the parasite has identified potential inhibitors, indicating the promise of using these compounds for developing novel antileishmanial drugs.
Article
Chemistry, Medicinal
Joas T. S. Coimbra, Pedro A. Fernandes, Maria J. Ramos
Summary: Due to antibiotic resistance, it is crucial to explore new antibiotics and/or strategies to counter resistance. This study used molecular dynamics simulations and quantum mechanics/molecular mechanics methods to investigate the degradation of a streptogramin B antibiotic by Vgb lyase and assess the impact of point mutations on the reaction. The findings provide valuable insights into the linearization reactions of cyclic antibiotics and aid in the development of novel strategies against antibiotic resistance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
How Chee Ong, Joao T. S. Coimbra, Maria J. Ramos, Bengang Xing, Pedro A. Fernandes, Felipe Garcia
Summary: Mitochondrial targeting is a promising strategy for treating various diseases, and Triphenylphosphonium (TPP+) moieties have been widely used for this purpose. However, the core structure of TPP+ remains largely unchanged, so this study explored the use of novel phosphorus-nitrogen based frameworks as mitochondrial delivery vectors. The phosphazenylphosphonium (PPN+) moiety was found to be highly effective in delivering cargo to mitochondria, with unique electronic properties and high lipophilicity.
Article
Chemistry, Multidisciplinary
Carola Jerves, Rui P. P. Neves, Saulo L. da Silva, Maria J. Ramos, Pedro A. Fernandes
Summary: The PETase enzyme from Ideonella sakaiensis can degrade PET at room temperature. Computational enzyme optimization can accelerate enzyme engineering. Mutations can stabilize transition states and decrease activation barriers. Rational enzyme engineering on PETase and other enzymes is encouraged.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Physical
Tatiana F. Vieira, Nuno M. F. S. A. Cerqueira, Manuel Simoes, Sergio F. Sousa
Summary: PqsD is an enzyme involved in the synthesis of essential secondary metabolites for Pseudomonas quinolone signal (PQS) inducer molecules. Inhibition of PqsD activity can inhibit biofilm formation and can be combined with PqsR inhibition. This study used computational methods to screen and select eight compounds as potential quorum sensing inhibitors.
MOLECULAR SYSTEMS DESIGN & ENGINEERING
(2024)