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Multidisciplinary Sciences
Krishna Neupane, Meng Zhao, Aaron Lyons, Sneha Munshi, Sandaru M. Ileperuma, Dustin B. Ritchie, Noel Q. Hoffer, Abhishek Narayari, Michael T. Woodside
Summary: The RNA pseudoknot of SARS-CoV-2 that induces programmed ribosomal frameshifting is a potential drug target. Through optical tweezer experiments, researchers identified two pseudoknotted conformers with distinct topologies and revealed the folding mechanism of the frameshift signal, shedding light on its conformational heterogeneity and implications for drug discovery based on structure.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Guimei Yu, Yunpeng Bai, Kunpeng Li, Ovini Amarasinghe, Wen Jiang, Zhong-Yin Zhang
Summary: This study characterized a dodecameric state of VCP and revealed the impact of nucleotide status on the conformation, as well as described a nucleotide status-dependent dodecamerization mechanism. The results highlight new intra- and inter-hexamer conformational changes dictated by nucleotide status, indicating a potential mechanism for controlling VCP oligomeric states.
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Biochemistry & Molecular Biology
Qingzhou Ma, Haiyan Wu, Yuehua Geng, Qiang Li, Rui Zang, Yashuang Guo, Chao Xu, Meng Zhang
Summary: The mitochondrial genomes of 56 C. cassiicola isolates were analyzed, revealing rich genetic variations and possible positive selection pressure on certain genes. Phylogenetic analysis showed diverse relationships among isolates, which had weak correlations with host range and toxin class. This study provides new insights into the intraspecific microevolution and genetic diversity of C. cassiicola.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Immunology
Wei Wei, Mitchell J. J. Geer, Xinyi Guo, Igor Dolgalev, Neville E. E. Sanjana, Benjamin G. G. Neel
Summary: SHP2 acts as an upstream regulator of RAS activation. Through CRISPR/Cas9 screening, LZTR1, MAP4K5, SPRED2/STK40, and INPPL1 were identified as novel genes associated with SHP2 resistance. Understanding the mechanisms of SHP2 resistance and identifying potential combination therapies is important for overcoming drug resistance in cancer treatment.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Kyle S. Gregory, Anna R. Newell, Otsile O. Mojanaga, Sai Man Liu, K. Ravi Acharya
Summary: This study determined the crystal structure of botulinum neurotoxin A6 cell binding domain (H-C/A6) in complex with GD1a and presented a new crystal form of wild type H-C/A6 (crystal form II), revealing the degree of conformational flexibility exhibited by H-C/A6.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Marine & Freshwater Biology
Lorenzo Longobardi, Laurent Dubroca, Diana Sarno, Adriana Zingone
Summary: This study examined the ecological niche of 10 globally distributed phytoplankton species and found significant variations in frequency, average abundance, and seasonal pattern among sites. The annual maxima of these species occurred within a wide range of physical-chemical variables, indicating a considerably wide global niche for each species. These findings should be taken into account when predicting species distributions in future scenarios of climate change.
JOURNAL OF PLANKTON RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Gabriela Martinez de la Escalera, Angel M. Segura, Carla Kruk, Badih Ghattas, Frederick M. Cohan, Andres Iriarte, Claudia Piccini
Summary: Studying the genetic diversity of toxic Microcystis aeruginosa complex (MAC) can help us understand their adaptability in different environments, explaining their success in various environmental conditions.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Laura C. Watkins, William F. DeGrado, Gregory A. Voth
Summary: The D44N mutation in the influenza A M2 channel opens the channel gate and increases proton conduction, leading to a loss of asymmetric conduction. This mutation lowers the energy barrier for His37 deprotonation in the activated state and facilitates proton flux through the Va127 tetrad. Increased hydration around the His37 tetrad enhances proton transport efficiency.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Chandrima Jash, Akiva Feintuch, Shira Nudelman, Nurit Manukovsky, Elwy H. Abdelkader, Sudeshna Bhattacharya, Gunnar Jeschke, Gottfried Otting, Daniella Goldfarb
Summary: This study compared the solution binding modes of MARCKS and IQ peptides with CaM using DEER and paramagnetic NMR techniques. It was found that MARCKS binding with CaM did not result in a closed conformation, while IQ binding generated a closed conformation. A solution structure model derived from elastic network modeling was in good agreement with the crystal structure.
Article
Multidisciplinary Sciences
Yiming Mao, Assane Hamidou Abdoulaye, Jiming Song, Xiaowen Yao, Yijie Zhang, Yu Gao, Yiwei Ye, Kai Luo, Wei Xia, Yinhua Chen
Summary: The AS2 gene plays a crucial role in the development of flat, symmetric, and extended leaf laminae and their veins. The AS2/LOB domain has been characterized in various plants, but its characteristics in cassava remain uncharacterized. This study identified 55 ASL/LBD genes in cassava and found that they may be involved in hormone and stress responses. The expression of MeASLBD46 and MeASLBD47 significantly responds to disease and drought stress in cassava.
Article
Biochemistry & Molecular Biology
Dongyun Xin, Yangyang Bai, Yi Bi, Libang He, Yuxin Kang, Chuanying Pan, Haijing Zhu, Hong Chen, Lei Qu, Xianyong Lan
Summary: IGF2BP2 gene mutation P4-Ins-13bp is significantly associated with goat litter size, with goats having the DD genotype producing more offspring. This mutation can be used as a potential molecular marker for selective breeding to improve economic efficiency in the goat industry.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2021)
Article
Genetics & Heredity
Fabian Meili, William J. Wei, Wun-Chey Sin, Warren M. Meyers, Iulia Dascalu, Daniel B. Callaghan, Sanja Rogic, Paul Pavlidis, Kurt Haas
Summary: SYNGAP1, a protein involved in regulating synaptic plasticity, has been linked to various neurological disorders. This study characterized 57 variants in multiple functional assays, revealing different impacts on protein function and stability. Variants within specific structural domains showed greater loss-of-function effects, while protein instability was a major factor for only two missense variants. High-content imaging identified subcellular localization differences that correlated with altered catalytic activity, indicating diverse molecular mechanisms underlying variant dysfunction. This multidimensional dataset provides insights for predicting the pathogenicity of SYNGAP1 variants.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biodiversity Conservation
Gary C. Longo, John Harms, John R. Hyde, Matthew T. Craig, Ana Ramon-Laca, Krista M. Nichols
Summary: The vermilion rockfish complex on the U.S. West Coast, composed of cryptic sister species vermilion and sunset rockfish, is a valuable recreational fishery. By using RADseq markers, researchers successfully differentiated between these two species and identified hybrid individuals. Genetic analyses revealed two weakly divergent genetic groups for sunset rockfish and three distinct genetic groups with stronger signals of differentiation for vermilion rockfish.
CONSERVATION GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Saeideh Nakhaei-Rad, Fatemeh Janatifard, Radovan Dvorsky, Mohammad R. R. Ahmadian, Mohammad R. R. Housaindokht
Summary: Germline mutations in the C-terminus of CRAF kinase, particularly L603, and S612T/L613V, are associated with congenital heart disorders, such as dilated cardiomyopathy and hypertrophic cardiomyopathy. The study investigates the impacts of these mutations on the conformation of the CRAF kinase domain and provides a mechanistic basis for the contradictory effects of the CRAF variants associated with different heart disorders.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Medicinal
Dimitrios Kolokouris, Iris E. Kalenderoglou, Antonios Kolocouris
Summary: Molecular dynamics simulations have accurately described the structure and interactions of the influenza A M2 protein in the membrane environment, providing valuable insights for viroporin systems and potential drug targets.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)