Article
Biochemistry & Molecular Biology
Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Jimin Pei, Nick Grishin
Summary: The Rossmann-like fold is a prevalent and diversified double-helical superstructure of ancient evolutionary origin, present in various metabolic enzymes; RLM-containing proteins constitute approximately 15% of the human proteome, with disease-causing mutations more frequent within RLM domains, highlighting their importance for human health.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Tongqing Li, Steven E. Stayrook, Yuko Tsutsui, Jianan Zhang, Yueyue Wang, Hengyi Li, Andrew Proffitt, Stefan G. Krimmer, Mansoor Ahmed, Olivia Belliveau, Ian X. Walker, Krishna C. Mudumbi, Yoshihisa Suzuki, Irit Lax, Diego Alvarado, Mark A. Lemmon, Joseph Schlessinger, Daryl E. Klein
Summary: The proto-oncogene ALK encodes anaplastic lymphoma kinase, which is primarily expressed in the developing nervous system. Its activity is associated with learning and memory, energy expenditure, and obesity prevention. Aberrant ALK signaling causes various cancers, including being a driver in pediatric neuroblastoma. The study reveals the crystal structures of ALK's extracellular glycine-rich domain (GRD) and how it regulates receptor activity, providing insights into potential therapeutics for ALK-expressing cancers.
Article
Biochemistry & Molecular Biology
Yizhou Yin, Matthew G. Romei, Kannan Sankar, Lipika R. Pal, Kam Hon Hoi, Yanli Yang, Brandon Leonard, Gladys De Leon Boenig, Nikit Kumar, Marissa Matsumoto, Jian Payandeh, Seth F. Harris, John Moult, Greg A. Lazar
Summary: This study analyzed and characterized the structural interactions of the antibody fragment antigen-binding (Fab) regions, leading to the discovery of previously unnoticed interfaces between antibodies. Experimental validation revealed the potential of these interfaces and provided new opportunities for their drug optimization.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biology
Tania Filipa Custodio, Peter Aasted Paulsen, Kelly May Frain, Bjorn Panyella Pedersen
Summary: The study compared the structures and functional data of GLUT1 and GLUT3, revealing significant differences in glucose affinity between them, possibly due to interactions between the cytosolic SP motif and conserved A motif. Additionally, previously undescribed Cl- ion site and endofacial lipid/glucose binding site in GLUT1 were identified as modulators of GLUT kinetics.
LIFE SCIENCE ALLIANCE
(2021)
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)
Review
Biochemical Research Methods
Carlos H. M. Rodrigues, Douglas E. Pires, Tom L. Blundell, David B. Ascher
Summary: Protein-protein interfaces have unique binding geometry and physicochemical properties, with concave binding sites that challenge the previous belief about their flatness. A comprehensive review of protein-protein interface landscape reveals the utilization of small binding pockets even in larger flat interfaces.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Mickael Machat, Florent Langenfeld, Daniela Craciun, Lea Sirugue, Taoufik Labib, Nathalie Lagarde, Maxime Maria, Matthieu Montes
Summary: Investigating the structure of biological systems at the molecular level can provide insights into their functions and dynamics. The shape and surface of biomolecules are crucial for molecular recognition events, and characterizing their geometry can enhance predictions of interactions. Evaluating shape retrieval methods from the computer vision community on protein shapes shows the importance of protein surface shape as a higher-level representation of protein structure, allowing for the identification of surficial homologs and potential interacting partners.
Article
Multidisciplinary Sciences
Rolando Hernandez, Julio C. Facelli
Summary: By comparing predicted structure-derived properties from wild type and mutated proteins using protein structure prediction methods, diverse structural changes were revealed, providing a new research avenue for understanding the impact of protein mutations on health.
Article
Biochemistry & Molecular Biology
Clinton Gabel, Zhuang Li, Heng Zhang, Leifu Chang
Summary: This study presents the cryo-EM structures of three type I-F Acr proteins bound to the Csy complex from Pseudomonas aeruginosa, revealing their mechanisms of inhibiting MGE degradation by binding to different sites on the Csy complex.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Khalique Newaz, Jacob Piland, Patricia L. Clark, Scott J. Emrich, Jun Li, Tijana Milenkovic
Summary: This study presents a novel approach for protein structural classification by modeling protein 3D structures as multi-layer sequential PSNs to capture 3D sub-structures. The results show that this approach outperforms existing methods.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Zhuangfeng Weng, Xinxin Shen, Jiefu Zheng, Huanhuan Liang, Yingfang Liu
Summary: DEPTOR serves as an endogenous inhibitor of the mTOR signaling pathway and dissociates from mTORC1 complex upon activation by phosphatidic acid. The N-terminal tandem DEP domains of DEPTOR fold into a dumbbell-shaped structure, which interacts directly with phosphatidic acid and is stabilized by a DDEX motif.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Sarika Kondra, Titli Sarkar, Vijay Raghavan, Wu Xu
Summary: Development of protein 3-D structural comparison methods is crucial for understanding protein functions, but existing methods have limitations. Researchers have developed a novel method based on Triangular Spatial Relationship (TSR), which accurately quantifies structural similarity and provides deeper insights into proteases and kinases.
FRONTIERS IN CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Sebastian Swanson, Venkatesh Sivaraman, Gevorg Grigoryan, Amy E. Keating
Summary: Despite the challenges in de novo design of small proteins or peptides that bind to a desired target, this study presents a method that utilizes tertiary motifs (TERMs) mined from known structures to construct custom peptide structures that complement a target surface. The results demonstrate that TERM-based seeds can accurately describe known binding structures and known peptide structures can be reconstructed with high accuracy from peptide-covering seeds. This method has potential in efficiently designing novel target-complementing binders.
Article
Biology
Titli Sarkar, Vijay V. Raghavan, Feng Chen, Andrew Riley, Sophia Zhou, Wu Xu
Summary: The study found that amino acid grouping can improve the accuracy of protein clustering and aid in the discovery of conserved structural motifs. Principal component analysis showed that amino acid grouping can reduce structure diversity, enhance the ability to capture structural variations, and shows promising prospects.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Denis V. Petrovskiy, Kirill S. Nikolsky, Vladimir R. Rudnev, Liudmila I. Kulikova, Tatiana V. Butkova, Kristina A. Malsagova, Arthur T. Kopylov, Anna L. Kaysheva
Summary: This article introduces a new tool called SAFoldNet, which uses neural networks to search and align protein structures. The study shows that this method is competitive in searching and aligning protein structures, and a user-friendly web interface service has been developed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)