Article
Chemistry, Medicinal
Feng-Xu Wu, Jing-Fang Yang, Long-Can Mei, Fan Wang, Ge-Fei Hao, Guang-Fu Yang
Summary: Protein-protein interactions are crucial in biological processes, and studying the mutational effects of hotspots helps understand protein binding. The PIIMS web server integrates molecular dynamics simulation and free energy perturbation to further evaluate the impact of different mutations on hotspot residues.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Swarnendu Tripathi, Nikita R. Dsouza, Angela J. Mathison, Elise Leverence, Raul Urrutia, Michael T. Zimmermann
Summary: This study reports computational scores for interpreting disease-associated genomic variation in the RAS family of genes. By using a combination of experimental datasets and computational methods, the research found a high correlation between 3D structure-based scores and experimental measures, indicating the impact of biochemical scores on the functional behavior of variants.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Biochemical Research Methods
Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli
Summary: This study discusses biases in predicting protein stability changes upon mutation, presents a more general perspective on the problem, and introduces a machine learning-based method that directly addresses the bias issue. Analysis shows that this method is nearly insensitive to the addressed problem.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agriculture, Multidisciplinary
Emma B. A. Hinderink, Claire C. Berton-Carabin, Karin Schroen, Alain Riaublanc, Berenice Houinsou-Houssou, Adeline Boire, Claude Genot
Summary: Proteins play a key role in stabilizing emulsions, with their molecular properties affecting their interfacial and emulsifying properties. Fluorescence spectroscopy can provide insights into protein conformation. Whey proteins and pea proteins show different behaviors in emulsions, with whey proteins adsorbing at the oil-water interface rich in Trp residues while pea proteins exhibit soluble aggregates with no changes in Trp residues upon emulsification.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemical Research Methods
Corrado Pancotti, Silvia Benevenuta, Giovanni Birolo, Virginia Alberini, Valeria Repetto, Tiziana Sanavia, Emidio Capriotti, Piero Fariselli
Summary: Predicting the difference in thermodynamic stability between protein variants is important for protein design and understanding genotype-phenotype relationships. This study introduces a new dataset and evaluates the prediction performance of 21 different tools. The results suggest that considering both direct and reverse variants improves the prediction accuracy.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Yelu Jiang, Lijun Quan, Kailong Li, Yan Li, Yiting Zhou, Tingfang Wu, Qiang Lyu
Summary: Effectively predicting protein-protein interactions after amino acid mutations is crucial for understanding protein function and designing drugs. This study proposes a deep graph convolution (DGC) network-based framework, DGCddG, which accurately predicts changes in protein-protein binding affinity after mutation. The model achieves good performance for both single and multi-point mutations, and shows promising results in predicting ACE2 changes in blind tests related to the SARS-CoV-2 virus.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Mehdi Kosaca, Irem Yilmazbilek, Ezgi Karaca
Summary: Mutation-induced changes across protein-protein interfaces often lead to severe diseases. To predict the impact of such mutations, computational tools like FoldX and EvoEF1 have been developed. We present PROT-ON, a framework that identifies critical protein interface mutations and provides a designer mutation set for designing new protein binders.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jan Velecky, Marie Hamsikova, Jan Stourac, Milos Musil, Jiri Damborsky, David Bednar, Stanislav Mazurenko
Summary: Protein solubility is crucial for protein production and manufacturing yields. Understanding the structural determinants of solubility and the effects of mutations can help connect human diseases with protein aggregation. The SoluProtMut(DB) database contains extensive data on protein solubility changes upon mutations, serving as a valuable resource for researchers designing improved protein variants and developing machine learning tools. The database includes previously published datasets and additional data from recent studies, and it has been curated for machine learning applications.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Engineering, Environmental
Yuechao Zhao, Xu Lei, Jia-nan Zheng, Ming Li, Michael L. Johns, Mingxing Huang, Yongchen Song
Summary: Gas hydrates are considered promising for gas storage, energy transportation, and seawater desalination. Using MRI, researchers were able to non-invasively image the formation of opaque hydrates from CO2 and water in a cylindrical vessel at low temperature and high pressure. They observed dense hydrate layers forming consistently at the gas-water interface, porous hydrate layers above it, and complex dendritic formations in the water phase below.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Chemistry, Physical
Ekaterina Maximova, Eugene B. Postnikov, Anastasia Lavrova, Vladimir Farafonov, Dmitry Nerukh
Summary: In this study, the dissociation of ligand isoniazid from a protein catalase was investigated using MD simulations, with a novel method proposed to extrapolate dissociation times to the zero-force limit for comparison with experimental values. The calculated dissociation time was found to quantitatively match the experimental value, despite the extrapolation over multiple orders of magnitude in time.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biology
Corentin Leger, Irene Pitard, Mirko Sadi, Nicolas Carvalho, Sebastien Brier, Ariel Mechaly, Dorothee Raoux-Barbot, Maryline Davi, Sylviane Hoos, Patrick Weber, Patrice Vachette, Dominique Durand, Ahmed Haouz, J. Inaki Guijarro, Daniel Ladant, Alexandre Chenal
Summary: We conducted a molecular characterization of CaM:CDZ complexes using SEC-SAXS, X-ray crystallography, HDX-MS, and NMR methods. The binding of CDZ causes conformational reorientation of CaM and stabilizes its structural elements, leading to reduced protein dynamics. Residues involved in the stabilization of the CaM:CDZ complex were identified. These findings provide insights into CDZ-induced dynamics and structural changes of CaM, which can be used for the design of more selective CaM antagonists.
Article
Biochemical Research Methods
Xiaojing Sui, Dezerae Cox, Shuai Nie, Gavin E. Reid, Danny M. Hatters
Summary: During the recovery from heat shock, eukaryotic cells rapidly down-regulate prefoldins and translation machinery, while mobilizing protein quality control mechanisms, changing cellular energy metabolism, translational activity, and actin cytoskeleton. Long-term adaptation to stress involves the renewal of core cellular components.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Longmei Li, Jin Zhang, Wenjing Sun, Weimin Gong, Changlin Tian, Pan Shi, Chaowei Shi
Summary: This study used F-19 solution NMR spectroscopy to investigate the conformational changes of G proteins upon interaction with detergent mimicking membrane and receptor. The results showed that there are two equilibrium states in the Gain apo states, and the interaction with detergents accelerates the conformational transformation.
CHINESE CHEMICAL LETTERS
(2022)
Article
Biochemical Research Methods
Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine Orengo
Summary: Mutations in human proteins can cause diseases. The structure of these proteins helps in understanding disease mechanisms and developing therapeutics. Advanced deep learning techniques allow us to predict protein structures even without structural homologs. By modeling and extracting domains, we predicted functional sites and analyzed disease-associated mutations. We found that a significant number of mutations were near functional sites, caused structural destabilization, and predicted to be pathogenic. Both the RoseTTAFold and AlphaFold models provided confidence in our predictions, and the combination of these models explained additional mutations.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Ambritha Balasundaram, C. George Priya Doss
Summary: The study reveals the impact of specific amino acid substitutions on the structure, function, and DNA-binding affinity of p53 protein, which is a vital regulator of tissue homeostasis. The findings suggest that these substitutions reduce the protein's affinity for DNA and may disrupt cell division, leading to a gain of p53 function and promoting cancer development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Mohindar M. Karunakaran, Carrie R. Willcox, Mahboob Salim, Daniel Paletta, Alina S. Fichtner, Angela Noll, Lisa Starick, Anna Noehren, Charlotte R. Begley, Katie A. Berwick, Raphael A. G. Chaleil, Vincent Pitard, Julie Dechanet-Merville, Paul A. Bates, Brigitte Kimmel, Timothy J. Knowles, Volker Kunzmann, Lutz Walter, Mark Jeeves, Fiyaz Mohammed, Benjamin E. Willcox, Thomas Herrmann
Article
Biology
Esther Wershof, Danielle Park, David J. Barry, Robert P. Jenkins, Antonio Rullan, Anna Wilkins, Karin Schlegelmilch, Ioannis Roxanis, Kurt Anderson, Paul A. Bates, Erik Sahai
Summary: Current tools for quantitative analysis of extracellular matrix patterns often focus on a single aspect, requiring the need for an automated pipeline that can comprehensively describe various patterns. The TWOMBLI plugin covers a wide range of metrics for matrix analysis, providing a versatile and user-friendly tool applicable to diverse cellular networks.
LIFE SCIENCE ALLIANCE
(2021)
Review
Plant Sciences
Carmen Castell, Luis A. Rodriguez-Lumbreras, Manuel Hervas, Juan Fernandez-Recio, Jose A. Navarro
Summary: The text discusses the evolution and functional differences of the copper-protein plastocyanin (Pc) among different groups of organisms, as well as the mechanisms of electron transfer in the green, red, and diatom lineages.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Ecology
Yue Zhao, Xiao Fu, Jose I. Lopez, Andrew Rowan, Lewis Au, Annika Fendler, Steve Hazell, Hang Xu, Stuart Horswell, Scott T. C. Shepherd, Lavinia Spain, Fiona Byrne, Gordon Stamp, Tim O'Brien, David Nicol, Marcellus Augustine, Ashish Chandra, Sarah Rudman, Antonia Toncheva, Lisa Pickering, Erik Sahai, James Larkin, Paul A. Bates, Charles Swanton, Samra Turajlic, Ben Challacombe, Simon Chowdhury, William Drake, Archana Fernando, Nicos Fotiadis, Andrew Furness, Emine Hatipoglu, Karen Harrison-Phipps, Peter Hill, Catherine Horsfield, Teresa Marafioti, Jonathon Olsburgh, Alexander Polson, Sergio Quezada, Mary Varia, Hema Verma, Kevin Litchfield
Summary: The study combines whole-tumour images and genomic data to reveal more aggressive subclonal growth and metastasizing subclones in the tumor center. Spatial dynamics strongly correlate with genomic alterations and play a significant role in tumor evolution.
NATURE ECOLOGY & EVOLUTION
(2021)
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
Physiology
Marica Muffoletto, Ahmed Qureshi, Aya Zeidan, Laila Muizniece, Xiao Fu, Jichao Zhao, Aditi Roy, Paul A. Bates, Oleg Aslanidi
Summary: Atrial fibrillation is a common cardiac arrhythmia with high morbidity and mortality rates, and catheter ablation is a first-line treatment option with suboptimal success rates. Computational approaches, combining image-based modeling and deep learning classifiers, show promise in assisting with CA therapy selection.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Ecology
Xiao Fu, Yue Zhao, Jose I. Lopez, Andrew Rowan, Lewis Au, Annika Fendler, Steve Hazell, Hang Xu, Stuart Horswell, Scott T. C. Shepherd, Charlotte E. Spencer, Lavinia Spain, Fiona Byrne, Gordon Stamp, Tim O'Brien, David Nicol, Marcellus Augustine, Ashish Chandra, Sarah Rudman, Antonia Toncheva, Andrew J. S. Furness, Lisa Pickering, Santosh Kumar, Dow-Mu Koh, Christina Messiou, Derfel ap Dafydd, Matthew R. Orton, Simon J. Doran, James Larkin, Charles Swanton, Erik Sahai, Kevin Litchfield, Samra Turajlic, Paul A. Bates
Summary: The study examined spatial and temporal features of clonal diversification in clear cell renal cell carcinoma using a combined modelling and real tumour analysis approach, providing insights into predicting tumour evolution patterns and subclone diversification levels.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Hannah Schmidbaur, Akane Kawaguchi, Tereza Clarence, Xiao Fu, Oi Pui Hoang, Bob Zimmermann, Elena A. Ritschard, Anton Weissenbacher, Jamie S. Foster, Spencer Nyholm, Paul A. Bates, Caroline B. Albertin, Elly Tanaka, Oleg Simakov
Summary: This study reveals the unique genomic, topological, and regulatory organization of cephalopod genomes, identifies microsyntenies associated with cephalopod nervous system evolution, and suggests that microsyntenic profiling will be central to understanding cephalopod innovations.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Elena Erausquin, Fabian Glaser, Juan Fernandez-Recio, Jacinto Lopez-Sagaseta
Summary: This study investigates the impact of a relevant mutation, Q498Y, present in currently circulating SARS-CoV-2 variants on the binding affinity between the spike receptor-binding domain (RBD) and ACE2. The results suggest that the Q498Y substitution increases the binding affinity and leads to stronger host-pathogen interactions.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Review
Biophysics
Shoshana J. Wodak, Sandor Vajda, Marc F. Lensink, Dima Kozakov, Paul A. Bates
Summary: This article discusses two intertwined disciplines in the protein structure prediction field: single chain modeling and complex modeling. The scientific developments in this field have been measured by small incremental steps, as observed through community-wide blind prediction experiments. However, recent dramatic advances in accurately predicting single protein chains have been made with the emergence of deep learning methodologies. The article reviews these breakthroughs and highlights the important role of blind prediction experiments in nurturing the structure prediction field. It also discusses how the new wave of artificial intelligence-based methods is impacting computational and experimental structural biology, and identifies future developments that deep learning methods are likely to lead to, provided that major challenges are overcome.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Multidisciplinary Sciences
Tereza Clarence, Nicolas S. M. Robert, Fatih Sarigol, Xiao Fu, Paul A. Bates, Oleg Simakov
Summary: Animal genomes are organized into conserved chromosomes that form distinct evolutionary units. By using chromosomal modeling, researchers have inferred the three-dimensional topology of animal genomes. They have identified evolutionarily conserved three-dimensional networks and novel interactors associated with known gene linkages. This evidence suggests that the spatial organization of animal genomes, termed spatiosynteny, plays a role in understanding the conservation of chromosomes.
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)
Correction
Immunology
Mohindar M. Karunakaran, Carrie R. Willcox, Mahboob Salim, Daniel Paletta, Alina S. Fichtner, Angela Noll, Lisa Starick, Anna Nohren, Charlotte R. Begley, Katie A. Berwick, Raphael A. G. Chaleil, Vincent Pitard, Julie Dechanet--Merville, Paul A. Bates, Brigitte Kimmel, Timothy J. Knowles, Volker Kunzmann, Lutz Wal-ter, Mark Jeeves, Fiyaz Mohammed, Benjamin E. Willcox, Thomas Herrmann
IMMUNOLOGICAL REVIEWS
(2023)
Meeting Abstract
Oncology
Xiao Fu, Ajay Bhargava, Sasha Bailey, Dhruva Biswas, Carlos Martinez Ruiz, Sunil Kumar, Paul French, Nicholas McGranahan, Charles Swanton, Paul A. Bates, Erik Sahai
Article
Biochemistry & Molecular Biology
Tereza Gerguri, Xiao Fu, Yasutaka Kakui, Bhavin S. Khatri, Christopher Barrington, Paul A. Bates, Frank Uhlmann
Summary: This study investigates two mechanisms, loop extrusion and diffusion capture, by using biophysical simulations to explore how SMC complexes organize chromatin. Results show that both mechanisms can lead to native-like contact probability distributions, but diffusion capture more readily reproduces mitotic chromosome axis shortening and chromatin compaction. Additionally, diffusion capture explains reduced and more anisotropic movements in mitotic chromatin and is supported by condensin distribution visualization within mitotic chromosomes.
NUCLEIC ACIDS RESEARCH
(2021)