Article
Computer Science, Artificial Intelligence
Marcelo B. A. Veras, Bishnu Sarker, Sabeur Aridhi, Joao P. P. Gomes, Jose A. F. Macedo, Engelbert Mephu Nguifo, Marie-Dominique Devignes, Malika Smail-Tabbone
Summary: Automatic protein function annotation is crucial for disease understanding and drug design. Similarity functions play an important role in protein function prediction, but there is a lack of specifically designed similarity functions for protein function annotation. This study analyzes the best similarity functions for the task and proposes a new one.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Biology
Oliviero Carugo
Summary: This study comprehensively analyzed the features of disulfide bonds (DBs) that bridge two protein chains in the Protein Data Bank, resulting in a structural atlas of intermolecular DBs. It was found that these DBs tend to occur between protein chains with different sequences but belonging to the same structural class. Intermolecular DBs are more solvent accessible and less distorted compared to intramolecular DBs, while showing similar B-factors. They are mainly found in beta strands and predominantly beta structures. These findings are valuable for protein modeling and design.
Article
Biochemistry & Molecular Biology
Rahul Kaushik, Kam Y. J. Zhang
Summary: The structural information of proteins plays a crucial role in understanding their functions and interactions. The protein structure prediction method ProFitFun-Meta combines various structural information to assess the quality of predicted model structures. It has been validated and benchmarked against current state-of-the-art methods, demonstrating its reliability and efficiency. ProFitFun-Meta has the potential to become an integral component of computational pipelines for protein modeling and design.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Sajid Iqbal, Farida Begum, Dorothy Wavinya Nyamai, Nasir Jalal, Peter Shaw
Summary: The study identifies high-risk nsSNPs in ANGPTL3 and ANGPTL8 genes that may contribute to cancer development. Protein-protein interaction analysis reveals a strong association of ANGPTL proteins with tumor-suppressor proteins. Gene-expression profiling analysis demonstrates downregulation of ANGPTL3 in sarcoma, cholangio carcinoma, kidney chromophobe carcinoma, kidney renal clear cell carcinoma, and kidney renal papillary cell carcinoma, and downregulation of ANGPTL8 in cholangio carcinoma, glioblastoma, and breast invasive carcinoma. Survival rate analysis indicates that both upregulation and downregulation of ANGPTL3 and ANGPTL8 are associated with low survival rates in various types of cancer.
Article
Biochemistry & Molecular Biology
Guillem Prats-Ejarque, Helena Lorente, Clara Villalba, Raul Anguita, Lu Lu, Sergi Vazquez-Monteagudo, Pablo Fernandez-Millan, Ester Boix
Summary: Bacterial resistance to antibiotics has led to the development of a hybrid enzyme with high antimicrobial and catalytic activities. After multiple improvements, the RNase 3/1-v3 chimera was designed, which exhibited enhanced antimicrobial and catalytic activities, as well as low cytotoxicity. Furthermore, the RNase 3/1-v3 chimera was able to effectively eradicate intracellular infection in macrophages and induce autophagy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Oliviero Carugo
Summary: The novel procedure RaSPDB uses multiple PDB subsets to estimate and compute the average value and standard error of a protein feature F.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Rakesh Trivedi, Hampapathalu Adimurthy Nagarajaram
Summary: This review discusses different aspects of disordered proteins and protein regions, as well as the experimental and computational methods used to characterize them. Additionally, the role of disordered proteins in diseases and their potential as drug targets are explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Zbigniew Wyzewski, Marcin Gradowski, Marianna Krysinska, Malgorzata Dudkiewicz, Krzysztof Pawlowski
Summary: This article introduces a new family of potential ADP-ribosyltransferases and their potential roles in cellular signaling and infection processes, with structural connections to the innate immune system.
Article
Biochemistry & Molecular Biology
Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, Gerard Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko F. Aoki-Kinoshita, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley, Jasmine Y. Young
Summary: The worldwide Protein Data Bank has collaborated with Global Phasing Ltd. and the Noguchi Institute to enhance validation reports for small molecules, including 2D diagrams and 3D electron density maps, to improve confidence in ligand conformation and interactions with macromolecules.
Review
Biochemistry & Molecular Biology
Anastassia Andreevna Vorobieva
Summary: After decades of progress in computational protein design, the focus has now shifted towards designing proteins that fold and function in lipid membranes. Successful de novo designs of simplified model membrane protein systems have helped elucidate fundamental principles of protein folding and interaction in the hydrophobic lipid environment. New methodological innovations, including machine learning approaches and experimental techniques, offer opportunities for advancing membrane protein design.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jack Turner, Sanja Abbott, Neli Fonseca, Lucas Carrijo, Amudha Kumari Duraisamy, Osman Salih, Zhe Wang, Gerard J. Kleywegt, Kyle L. Morris, Ardan Patwardhan, Stephen K. Burley, Gregg Crichlow, Zukang Feng, Justin W. Flatt, Sutapa Ghosh, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan, Chenghua Shao, Jasmine Young, Sameer Velankar, David Armstrong, Marcus Bage, Wesley Morellato Bueno, Genevieve Evans, Romana Gaborova, Sudakshina Ganguly, Deepti Gupta, Deborah Harrus, Ahsan Tanweer, Manju Bansal, Vetriselvi Rangannan, Genji Kurisu, Hasumi Cho, Yasuyo Ikegawa, Yumiko Kengaku, Ju Yaen Kim, Satomi Niwa, Junko Sato, Ayako Takuwa, Jian Yu, Jeffrey C. Hoch, Kumaran Baskaran, Wenqing Xu, Weizhe Zhang, Xiaodan Ma
Summary: This article provides an overview of the Electron Microscopy Data Bank (EMDB), its significance as a global public archive, and its current holdings, recent updates, and future plans.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Pedro B. P. S. Reis, Djork-Arne Clevert, Miguel Machuqueiro
Summary: pK(a) values and isoelectric points of proteins can be estimated using computational methods with high accuracy, and the pKPDB database provides a vast amount of theoretical pK(a) values for over 120k protein structures. This database complements experimental data and provides insights on buried residues that are not well-represented in experimental measurements.
Article
Biochemistry & Molecular Biology
Christine Zardecki, Shuchismita Dutta, David S. Goodsell, Robert Lowe, Maria Voigt, Stephen K. Burley
Summary: PDB-101 is an online portal created to support education, research, and promotion of structural biology and protein science. It provides materials for exploring atomic-level three-dimensional structures of biomolecules and aims to train the next generation of users.
Article
Biology
Gonzalez Louisa Somermeyer, Aubin Fleiss, Alexander S. Mishin, Nina G. Bozhanova, Anna A. Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina Putintseva, Karen S. Sarkisyan, Fyodor A. Kondrashov
Summary: Studies on protein fitness landscapes help predict functional proteins, but the lack of systematic data on proteins with defined evolutionary relationships limits the generalization of these findings. We studied the fitness peaks of four orthologous fluorescent proteins and found that some peaks were sharp while others were flat.
Article
Biochemistry & Molecular Biology
Luciana Esposito, Nicole Balasco, Luigi Vitagliano
Summary: Oligomerization plays an important role in conferring certain properties to proteins. This study utilized the machine-learning algorithms implemented in AlphaFold to predict the structural states of functional oligomers in the KCTD protein family. The findings identified reliable three-dimensional models for several pentameric states that were previously uncharacterized from a structural point of view. The study provides a comprehensive view of KCTD protein oligomerization and offers insights into key biological processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Dawn Kohrt, Jennifer Crary, Marc Zimmer, Aaron N. Patrick, Heide L. Ford, Philip W. Hinds, Martha J. Grossel
Article
Chemistry, Multidisciplinary
Marc Zimmer
CHEMICAL & ENGINEERING NEWS
(2008)
Article
Chemistry, Physical
Nathan P. Lemay, Alicia L. Morgan, Elizabeth J. Archer, Luisa A. Dickson, Colleen M. Megley, Marc Zimmer
Article
Chemistry, Physical
Binsen Li, Ramza Shahid, Paola Peshkepija, Marc Zimmer
Article
Chemistry, Physical
Matthew H. Zimmer, Binsen Li, Ramza Shahid, Paola Peshkepija, Marc Zimmer
Review
Chemistry, Multidisciplinary
Marc Zimmer
CHEMICAL SOCIETY REVIEWS
(2009)
Review
Chemistry, Inorganic & Nuclear
Marc Zimmer
COORDINATION CHEMISTRY REVIEWS
(2009)
Article
Chemistry, Physical
Colleen M. Megley, Luisa A. Dickson, Scott L. Maddalo, Gabriel J. Chandler, Marc Zimmer
JOURNAL OF PHYSICAL CHEMISTRY B
(2009)
Article
Chemistry, Physical
Alex A. Samma, Chelsea K. Johnson, Shuang Song, Samuel Alvarez, Marc Zimmer
JOURNAL OF PHYSICAL CHEMISTRY B
(2010)
Article
Biochemistry & Molecular Biology
Justin Nwafor, Christian Salguero, Franceine Welcome, Sercan Durmus, Rachel N. Glasser, Marc Zimmer, Tanya L. Schneider
Summary: Studies have shown that the conserved glycines Gly31, 33, and 35 are essential for maintaining the integrity of the fluorescent protein structure, while molecular dynamics simulations indicate that mutating these glycines to alanine does not reduce chromophore formation.
Article
Biochemistry & Molecular Biology
Bruce R. Branchini, Danielle M. Ablamsky, Julie M. Rosenman, Lerna Uzasci, Tara L. Southworth, Marc Zimmer
Article
Chemistry, Inorganic & Nuclear
C Mbofana, M Zimmer
INORGANIC CHEMISTRY
(2006)
Article
Biochemistry & Molecular Biology
SL Maddalo, M Zimmer
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2006)
Article
Biochemistry & Molecular Biology
BR Branchini, TL Southworth, MH Murtiashaw, SR Wilkinson, NF Khattak, JC Rosenberg, M Zimmer