Article
Biochemistry & Molecular Biology
Miao Tian, Hongwei Li, Xiao Yan, Jing Gu, Pengfei Zheng, Sulan Luo, Dongting Zhangsun, Qiong Chen, Qin Ouyang
Summary: This study describes the design of new peptide inhibitors with higher binding affinity for postsynaptic density protein 95 (PSD95) using molecular dynamics simulations. The results show that enhancing hydrophobic interactions is an important strategy for the design of inhibitory peptides targeting PSD95. The synthesized peptides exhibited higher binding affinity compared to the original peptide, and F10W was identified as the most potent inhibitor.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki
Summary: With the powerful computation power of the Fugaku supercomputer, ab initio fragment molecular orbital calculations were performed for dynamic structures of protein-ligand complexes. By analyzing interfragment interaction energies and utilizing principal component analysis, the study revealed the dynamically cooperative interactions between the ligand and the residues, providing new insights into structure-based drug discovery.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemical Research Methods
Yumeng Yan, Sheng-You Huang
Summary: DeepHomo, a deep learning model for predicting inter-protein residue-residue contacts, integrates various information sources and achieves high precision, outperforming existing methods on both experimentally determined structures and simulated targets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Mahesh Kumar Teli, Surendra Kumar, Dharmendra Kumar Yadav, Mi-hyun Kim
Summary: This study identified a potential human PHD2 inhibitor for the treatment of oxidative/ischemic stress conditions through virtual screening and molecular simulation methods, indicating a novel therapeutic strategy for AD treatment.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Felipe Engelberger, Jonathan D. Zakary, Georg Kuenze
Summary: Recent developments in machine learning have led to significant progress in protein design. However, accurately evaluating the contributions of amino acid mutations to protein stability remains challenging. This study presents an interactive workflow called ENDURE that assesses the energetic effects of single and multiple mutations in proteins. ENDURE integrates various algorithms to analyze energy contributions and provides a web application for easy interpretation and visualization. The tool effectively identified mutations that improved the thermodynamic stability of a designed PET-degrading enzyme. Overall, ENDURE is a valuable resource for protein design and optimization researchers and practitioners.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jose A. Villegas, Tasneem M. Vaid, Michael E. Johnson, Terry W. Moore
Summary: A major challenge in computational modeling of macromolecules is the vast conformational space due to atomic degrees of freedom. Recent interest in predictive models of complexes mediated by PROTACs led to the application of advanced computational techniques. However, repurposing existing tools for protein-protein docking and linker conformer generation results in incompatible structures. In this study, a cyclic coordinate descent algorithm was used to position PROTACs into complex-bound configurations, allowing for a restricted search in protein-protein conformations that can be bridged by a PROTAC molecule with a given linker composition.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Physics, Multidisciplinary
Hao Li, Sheng-You Huang
Summary: Predicting protein-protein complex structures is crucial for understanding cellular processes and designing drugs. By incorporating experimental data and deep learning methods, the accuracy of protein-protein docking can be improved. The HDOCKsite method shows significant enhancement in docking performance.
Article
Biochemistry & Molecular Biology
Autum R. Baxter-Koenigs, Gina El Nesr, Doug Barrick
Summary: Singular value decomposition (SVD) of multiple sequence alignments (MSAs) is an important method for identifying and extracting features of sequence subgroups that are related to protein structure, function, stability, and taxonomy. This article provides a comprehensive description of the mathematics behind SVD and demonstrates its application through examples and analysis of protein families. Python scripts for SVD analysis of MSAs are also provided.
Article
Spectroscopy
Priyanka Mukherjee, Titas Kumar Mukhopadhyay, Manini Mukherjee, Pritam Roy, Rina Ghosh, Pinki Saha Sardar, Sanjib Ghosh
Summary: Conventional steady state and time resolved fluorescence studies are not effective in identifying specific tryptophan residues involved in the interaction between a multitryptophan protein and a quencher. This study demonstrates the involvement of buried Trp 310 residue and Tyr 320 residue in the interaction with acrylamide using low temperature phosphorescence spectra and molecular docking studies.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2024)
Article
Chemistry, Medicinal
Rupeng Dai, Xueting Bao, Ying Zhang, Yan Huang, Haohao Zhu, Kundi Yang, Bo Wang, Hongmei Wen, Wei Li, Jian Liu
Summary: In this study, hot-spot residues of ERα were identified using pharmacophore modeling, molecular mechanics/generalized Born surface area (MM/GBSA), and amino-acid mutation. Hit fragments were virtually screened and linked to generate compounds, among which compound B1 showed potential for breast cancer treatment.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Beata Szala-Mendyk, Andrzej Molski
Summary: This article investigates the molecular mechanism of fibril formation and finds that side chain geometry and terminal capping influence the propensity for fibrillation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Fatemeh Bamdad, Hossein Farrokhpour, Mahmud Ashrafizaadeh, Bijan Najafi
Summary: In this study, the SAPT (DFT) method was used to analyze the electronic interaction energies between flavonoids and the active site of Escherichia coli DNA Gyr. The results showed a significant correlation between the interaction energies and the biological activity of the flavonoids.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2022)
Article
Energy & Fuels
P. Kumar, P. M. Subbarao, L. D. Kala, V. K. Vijay
Summary: The thermal degradation characteristics of eucalyptus, pearl millet cob, and corncob were investigated using the nonisothermal thermogravimetric method to understand their thermal devolatilization behavior and estimation of various thermophysical properties. The activation energy using the Flynn-Wall-Ozawa method has been estimated and corncob was found to be the easiest for thermochemical conversion among the three biomasses. The TG analysis and activation energy indicated the favorable conversion properties of corncob.
JOURNAL OF ENERGY RESOURCES TECHNOLOGY-TRANSACTIONS OF THE ASME
(2021)
Article
Multidisciplinary Sciences
Yunfeng Li, Yulia Pustovalova, Tzanko I. Doukov, Jeffrey C. Hoch, Richard E. Mains, Betty A. Eipper, Bing Hao
Summary: The gated entry of lipophilic ligands into the enclosed hydrophobic pocket in stand-alone Sec14 domain proteins often links lipid metabolism to membrane trafficking. Similar domains occur in multidomain mammalian proteins that activate small GTPases and regulate actin dynamics. The neuronal RhoGEF Kalirin, a central regulator of cytoskeletal dynamics, contains a Sec14 domain (Kal(bSec14)) followed by multiple spectrin-like repeats and catalytic domains. Previous studies demonstrated that Kalirin lacking its Sec14 domain fails to maintain cell morphology or dendritic spine length, yet whether and how Kal(bSec14) interacts with lipids remain unknown. Here, we report the structural and biochemical characterization of Kal(bSec14) which adopts a closed conformation, sealing off the canonical ligand entry site, and instead employs a surface groove to bind a limited set of lysophospholipids. The low-affinity interactions of Kal(bSec14) with lysolipids are expected to serve as a general model for the regulation of Rho signaling by other Sec14-containing Rho activators.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Nitin Kumar Verma, Neera Raghav
Summary: In the realm of enzymes, the Enzyme Immobilization technique can be extremely beneficial. More research into computational approaches could lead to a better understanding as well as lead us in the direction of a more environmentally friendly and greener path. This study used molecular modelling techniques to investigate the immobilization of Lysozyme on Dialdehyde Cellulose. The results showed that lysine was the most likely amino acid residue to interact with dialdehyde cellulose. Different docking programs were used to analyze the binding affinity and interaction similarity of modified lysozyme with its substrate.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemical Research Methods
Jorge Roel-Touris, Alexandre M. J. J. Bonvin, Brian Jimenez-Garcia
Article
Biochemistry & Molecular Biology
Mireia Rosell, Luis A. Rodriguez-Lumbreras, Miguel Romero-Durana, Brian Jimenez-Garcia, Lucia Diaz, Juan Fernandez-Recio
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Francesco Ambrosetti, Brian Jimenez-Garcia, Jorge Roel-Touris, Alexandre M. J. J. Bonvin
Article
Biochemistry & Molecular Biology
Marc F. Lensink, Guillaume Brysbaert, Theo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A. G. Chaleil, Tereza Clarence, Paul A. Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S. Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Gieldon, Mateusz Kogut, Agnieszka G. Lipska, Adam Liwo, Emilia A. Lubecka, Martyna Maszota-Zieleniak, Adam K. Sieradzan, Rafal Slusarz, Patryk A. Wesolowski, Karolina Zieba, Carlos A. Del Carpio Munoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J. Gray, Alexandre M. J. J. Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jimenez-Garcia, Panagiotis I. Koukos, Siri Van Keulen, Charlotte W. Van Noort, Manon Reau, Jorge Roel-Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A. Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A. Rodriguez-Lumbreras, Juan Fernandez-Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng-You Huang, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G. Pierce, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda-Shitaka, Petras J. Kundrotas, Amar Singh, Ilya A. Vakser, Justas Dapkunas, Kliment Olechnovic, Ceslovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J. Wodak
Summary: The results of the CAPRI Round 50 showed that 25 groups participated in submitting models for 12 targets, with a good level of accuracy overall.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Rodrigo Honorato, Panagiotis Koukos, Brian Jimenez-Garcia, Andrei Tsaregorodtsev, Marco Verlato, Andrea Giachetti, Antonio Rosato, Alexandre M. J. J. Bonvin
Summary: Structural biology focuses on studying the structural and dynamic properties of biological macromolecules at atomic level, which is crucial for understanding cellular processes and has applications in health and food sciences. The WeNMR project has provided web-based services and high throughput computing infrastructure to over 23,000 users worldwide for 10 years, facilitating complex workflows in structural biology research.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Microbiology
Ferran Tarres-Freixas, Benjamin Trinite, Anna Pons-Grifols, Miguel Romero-Durana, Eva Riveira-Munoz, Carlos avila-Nieto, Monica Perez, Edurne Garcia-Vidal, Daniel Perez-Zsolt, Jordana Munoz-Basagoiti, Dalia Raich-Regue, Nuria Izquierdo-Useros, Cristina Andres, Andres Anton, Tomas Pumarola, Ignacio Blanco, Marc Noguera-Julian, Victor Guallar, Rosalba Lepore, Alfonso Valencia, Victor Urrea, Julia Vergara-Alert, Bonaventura Clotet, Ester Ballana, Jorge Carrillo, Joaquim Segales, Julia Blanco
Summary: The study found that the emerging SARS-CoV-2 variants show heterogeneous infectivity and pathogenesis in mice models, with B.1.351/Beta variant being the most pathogenic and BA.1.1/Omicron leading to lower viral RNA levels.
FRONTIERS IN MICROBIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Jessica Andreani, Masahito Ohue, Brian Jimenez-Garcia
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Virology
Leira Fernandez-Bastit, Nuria Roca, Miguel Romero-Durana, Jordi Rodon, Guillermo Cantero, Oscar Garcia, Carlos Lopez, Monica Perez, Rosa Lopez, Jorge Carrillo, Nuria Izquierdo-Useros, Julia Blanco, Bonaventura Clotet, Joan Pujols, Julia Vergara-Alert, Joaquim Segales, Cristina Lorca-Oro
Summary: This study investigated the susceptibility of goats to the B.1.351/Beta variant of SARS-CoV-2. The results showed evidence of infection in experimental inoculation, but the viral amount and tissue distribution suggested a low susceptibility of goats to this variant. Therefore, goats are unlikely to serve as reservoir species for SARS-CoV-2, and they are not suitable surrogates for studying SARS-CoV-2 infection in farmed animals.
Article
Biochemistry & Molecular Biology
Luis Angel Rodriguez-Lumbreras, Brian Jimenez-Garcia, Silvia Gimenez-Santamarina, Juan Fernandez-Recio
Summary: Protein-DNA interactions play essential roles in cellular processes, but there is a limited number of protein-DNA complex structures in current databases and a lack of computational methods for modeling their structures. In this study, a web server called pyDockDNA is presented, which can successfully predict protein-DNA complex structures with reasonable accuracy.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Carlos Lopez-Robles, Stefano Scaramuzza, Elsa N. Astorga-Simon, Morie Ishida, Chad D. Williamson, Soledad Banos-Mateos, David Gil-Carton, Miguel Romero-Durana, Ander Vidaurrazaga, Juan Fernandez-Recio, Adriana L. Rojas, Juan S. Bonifacino, Daniel Castano-Diez, Aitor Hierro
Summary: Using cryo-electron tomography, Lopez-Robles, Scaramuzza, Astorga-Simon, Ishida et al. solve the architecture of ESCPE-1, a protein scaffold that mediates the recycling of cargo from endosome to trans-Golgi network and plasma membrane in tubular carriers. The study reveals that ESCPE-1 has a single-layer coat organization and suggests that synergistic interactions between ESCPE-1 protomers, phosphoinositides, and cargo molecules drive tubule formation.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Brian Jimenez-Garcia, Jorge Roel-Touris, Didier Barradas-Bautista
Summary: The LightDock Server is a web server for integrative modeling of macromolecular interactions, offering ease of use and improved user experience.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Medicinal
Gilberto P. Pereira, Brian Jimenez-Garcia, Riccardo Pellarin, Guillaume Launay, Sangwook Wu, Juliette Martin, Paulo C. T. Souza
Summary: Proteolysis targeting chimeras (PROTACs) are emerging as a promising therapeutic approach for cancer treatment. This study presents a computational method that combines docking, energy scoring, and solvent-accessible surface distance filtering to generate PROTAC-compatible protein-protein interaction interfaces even in the absence of known PROTAC ligands.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Brian Jimenez-Garcia, Joao M. C. Teixeira, Mikael Trellet, Joao P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
Summary: The Protein Data Bank (PDB) file format, widely used in representing macromolecular structures, can now be manipulated through the flexible online service PDB-Tools Web, which offers a user-friendly graphical interface and more than 40 individual tools for users to mix-and-match. Complex pipelines can be easily executed and the resulting processed PDB files can be visualized and downloaded online.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)