Article
Multidisciplinary Sciences
Corey A. H. Allard, Guipeun Kang, Jeong Joo Kim, Wendy A. Valencia-Montoya, Ryan E. Hibbs, Nicholas W. Bellono
Summary: Chemotactile receptors (CRs) are a cephalopod-specific innovation that allow octopuses to explore the seafloor via 'taste by touch'. This study investigates the structural basis of sensory receptor evolution by comparing the cryo-electron microscopy structures of octopus CRs and nicotinic receptors. The findings show that while the channel architecture involved in cation permeation and signal transduction is conserved, the orthosteric ligand-binding site undergoes diversifying selection, enabling the detection of new molecules.
Article
Multidisciplinary Sciences
Andreas Lange, Prajal H. Patel, Brennen Heames, Adam M. Damry, Thorsten Saenger, Colin J. Jackson, Geoffrey D. Findlay, Erich Bornberg-Bauer
Summary: By analyzing the function and structure of the gene goddard, which emerged de novo at least 50 million years ago within the Drosophila genus, it was found that the protein structure has remained largely unchanged over millions of years of evolution.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Elizabeth M. Corteselli, Mona Sharafi, Robert Hondal, Maximilian MacPherson, Sheryl White, Ying-Wai Lam, Clarissa Gold, Allison M. Manuel, Albert van der Vliet, Severin T. Schneebeli, Vikas Anathy, Jianing Li, Yvonne M. W. Janssen-Heininger
Summary: This study provides insights into the mechanisms of oxidative inactivation of GLRX through molecular modeling and biochemical validation. The study identifies C8 and C83 as target sites for S-glutathionylation and oxidation, with C8 playing a prominent role in dimer formation and aggregation. Combinatorial mutation of C8, C26, and C83 results in increased activity of GLRX and resistance to oxidative inactivation and aggregation.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Sofiyah Shaibullah, Nurshahirah Shuhaimi, De-Sheng Ker, Nurhikmah Mohd-Sharif, Kok Lian Ho, Aik-Hong Teh, Jitka Waterman, Thean-Hock Tang, Rui-Rui Wong, Sheila Nathan, Rahmah Mohamed, Min Jia Ng, Shin-Yee Fung, Mohd Anuar Jonet, Mohd Firdaus-Raih, Chyan Leong Ng
Summary: BPSL1038 is a hypothetical protein found in Burkholderia pseudomallei with nuclease activity. Its structure is similar to known Cas2 nucleases, suggesting a common ancestor.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Phil Huss, Anthony Meger, Megan Leander, Kyle Nishikawa, Srivatsan Raman
Summary: The study systematically dissected the functional role of every residue in the tip domain of T7 phage RBP. Substitution patterns revealed host-specific differences and molecular adaptation to individual hosts. Gain-of-function and host-constricting variants were discovered, showcasing the therapeutic utility of engineered T7 variants against a urinary tract pathogen.
Article
Biochemical Research Methods
Tong Zhou, Jie Rong, Yang Liu, Weikang Gong, Chunhua Li
Summary: In this study, a new method called SREPRHot is proposed to predict binding hotspots in protein-RNA interactions. The method utilizes Synthetic Minority Over-sampling Technique (SMOTE) to handle dataset imbalance and introduces new features and a feature selection strategy. Experimental results show that SREPRHot achieves good performance on an independent testing dataset, demonstrating promising application potential.
Article
Multidisciplinary Sciences
Georgios E. Premetis, Angeliki Stathi, Anastassios C. Papageorgiou, Nikolaos E. Labrou
Summary: Multidrug-resistant (MDR) bacteria, especially Enterococcus faecium, pose a significant threat to public health. In this study, a potential peptidoglycan-degrading enzyme (PDE), EfAmi1, was identified in the E. faecium genome. EfAmi1 showed strong lytic and antimicrobial activities against clinically isolated bacterial pathogens. The crystal structure of the N-terminal amidase-2 domain in EfAmi1 was determined, revealing its potential as a promising new antimicrobial agent in the post-antibiotic era.
SCIENTIFIC REPORTS
(2023)
Article
Neurosciences
Sanjay Ghosh, Ashish Raj, Srikantan S. Nagarajan
Summary: This article introduces a computational framework that reconstructs functional connectivity from structural connectivity by identifying a joint subspace of eigenmodes. It is found that a small number of these eigenmodes are sufficient for reconstruction and the proposed algorithm shows competitive performance and better interpretability compared to existing methods.
Article
Microbiology
Morgan N. Price, Adam P. Arkin
Summary: To assist biologists in studying the functional residues of proteins, we developed two interactive web-based tools, SitesBLAST and Sites on a Tree. These tools identify homologs with known functional residues and show whether these residues are conserved. Additionally, Sites on a Tree visually displays how functional residues vary across a protein family. These tools provide valuable insights for predicting protein function and comparing key residues among similar proteins.
Article
Behavioral Sciences
Petr Sojka, Matej Slovak, Gabriela Vechetova, Robert Jech, David L. Perez, Tereza Serranova
Summary: This study investigates the gray matter volumetric profiles in functional movement disorder (FMD) and their relationship with resting-state functional connectivity (rsFC) profiles. The study finds that FMD is a multinetwork disorder and symptom severity-related structural alterations are mapped onto multiple brain regions, with an important role for the temporoparietal junction and its related connectivity.
BRAIN AND BEHAVIOR
(2022)
Article
Biochemistry & Molecular Biology
Shrivaishnavi Ranganathan, Deepa Sethi, Sandhya Kasivisweswaran, L. Ramya, Richa Priyadarshini, Ragothaman M. Yennamalli
Summary: This study presents a computational model and experimental evidence of the ars gene cluster in Deinococcus indicus DR1, revealing its role and regulation in arsenic resistance. The proteins in this cluster are involved in transcriptional regulation and reduction reactions to facilitate arsenic extrusion. This structural characterization study provides valuable insights into the mechanism of arsenic tolerance in Deinococcus indicus DR1.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Ian Sillitoe, Nicola Bordin, Natalie Dawson, Vaishali P. Waman, Paul Ashford, Harry M. Scholes, Camilla S. M. Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen, Mahnaz Abbasian, Sean Le Cornu, Su Datt Lam, Karel Berka, Ivana Hutarova Varekova, Radka Svobodova, Jon Lees, Christine A. Orengo
Summary: CATH identifies protein domains in structures and classifies them into evolutionary superfamilies, providing structural and functional annotations. The latest release significantly increases coverage of structural and sequence data, with additional derived data such as predicted sequence domains and functionally coherent sequence subsets. The FunFam generation pipeline has been re-engineered to capture more sequences with increased functional purity and information content.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Zhongjie Liang, Tonghai Liu, Qi Li, Guangyu Zhang, Bei Zhang, Xikun Du, Jingqiu Liu, Zhifeng Chen, Hong Ding, Guang Hu, Hao Lin, Fei Zhu, Cheng Luo
Summary: This study applies a deep neural network model to assign functional phosphosites, and confirms that NADK-S48/50 phosphorylation is associated with the activation of its enzymatic activity, with ERK1/2 identified as the primary kinases responsible. FuncPhos-SEQ is also developed as an online server.
Article
Dermatology
Aditi Chandra, Shantanab Das, Sayani Mazumder, Swapan Senapati, Gobinda Chatterjee, Raghunath Chatterjee
Summary: This study identified a regulatory SNP at the enhancing region of the LCE3A gene which interacts epistatically with HLA-Cw6. The findings shed light on the control role of signal transducer and activator of transcription 3 in this region, as well as its mechanism in psoriasis pathogenesis.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yui Kawamura, Chiharu Ishida, Ryo Miyata, Azusa Miyata, Seiichiro Hayashi, Daisuke Fujinami, Sohei Ito, Shogo Nakano
Summary: This study designed a novel L-amino acid oxidase, HTAncLAAO2, with high thermostability and long-term stability through ancestral sequence reconstruction. The crystal structure of HTAncLAAO2 was determined, showing an octameric form. Enzymatic property analysis revealed that HTAncLAAO2 has significantly higher catalytic efficiency towards four L-amino acids compared to L-Trp. A variant of HTAncLAAO2, HTAncLAAO2(W220A), was obtained with over 6-fold increase in catalytic efficiency towards L-Trp, making it suitable for synthesizing enantio-pure D-Trp derivatives.
COMMUNICATIONS CHEMISTRY
(2023)
Review
Mathematical & Computational Biology
Kiyoko F. Aoki-Kinoshita, Akira R. Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi-an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao, Shuichi Kawashima, Shinobu Okamoto, Toshiaki Katayama, Soichi Ogishima
JOURNAL OF BIOMEDICAL SEMANTICS
(2015)
Article
Biochemistry & Molecular Biology
Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
NUCLEIC ACIDS RESEARCH
(2017)
Article
Chemistry, Multidisciplinary
Gert-Jan Bekker, Haruki Nakamura, Akira R. Kinjo
JOURNAL OF CHEMINFORMATICS
(2016)
Article
Mathematical & Computational Biology
Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
JOURNAL OF BIOMEDICAL SEMANTICS
(2016)
Article
Biochemistry & Molecular Biology
Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata, Naohiro Kobayashi, Toshimichi Fujiwara, Genji Kurisu, Haruki Nakamura
Article
Biochemical Research Methods
Damien Hall, Akira R. Kinjo, Yuji Goto
ANALYTICAL BIOCHEMISTRY
(2018)
Article
Biology
Akira R. Kinjo
JOURNAL OF THEORETICAL BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Akira R. Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, Atsushi Nakagawa, Haruki Nakamura
NUCLEIC ACIDS RESEARCH
(2012)
Article
Multidisciplinary Sciences
Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, Akira R. Kinjo
Article
Biochemistry & Molecular Biology
Bhaskar Dasgupta, Haruki Nakamura, Akira R. Kinjo
Article
Biochemistry & Molecular Biology
Yoichi Murakami, Kengo Kinoshita, Akira R. Kinjo, Haruki Nakamura
Article
Biochemistry & Molecular Biology
Bhaskar Dasgupta, Haruki Nakamura, Akira R. Kinjo
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2014)
Review
Mathematical & Computational Biology
Toshiaki Katayama, Mark D. Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul J. P. Bonnal, Brad Chapman, Peter J. A. Cock, Tore Eriksson, Paul M. K. Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L. Saito, Matthias Samwald, Venkata P. Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Matthias Samwald, Venkata P. Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A. Vos, David Withers, Chisato Yamasaki, Christian M. Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi
JOURNAL OF BIOMEDICAL SEMANTICS
(2013)
Review
Biophysics
Eden Tian Hwa Ng, Akira R. Kinjo
Summary: Plasticity-led evolution is a form of evolution that induces novel traits through phenotypic plasticity and maintains them over generations through genetic adaptation in response to environmental changes. Computational models, such as gene regulatory network models, are useful in understanding the underlying mechanisms and making predictions about this type of evolution.
BIOPHYSICAL REVIEWS
(2022)
Article
Biochemical Research Methods
Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R. Kinjo, Nuria Queralt-Rosinach, Robert Hoehndorf
