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BPS2025 - Exploring the interaction between Kv2.1 and auxiliary AMIGO subunits using computational and experimental approaches

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Biophysical Journal 2025年第3期124卷 602a-602a页

作者： Adrian Koretsky Ana I. Fernández-Mariño Vanessa Leone Xiaofeng Tan Lucy R. Forrest Kenton Swartz National Institute of Neurological Disorders and Stroke National Institutes of Health Bethesda MD USA Molecular Physiology and Biophysics Section National Institute of Neurological Disorders and Stroke National Institutes of Health Bethesda MD USA Computational Structural Biology Section National Institute of Neurological Disorders and Stroke National Institutes of Health Bethesda MD USA National Institutes of Health Bethesda MD USA

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Author Correction: Efficient genetic code expansion without host genome modifications

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Nature biotechnology 2024年 2024 Oct 7页

作者： Alan Costello Alexander A Peterson David L Lanster Zhiyi Li Gavriela D Carver Ahmed H Badran Department of Chemistry The Scripps Research Institute La Jolla CA USA. Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA USA. Doctoral Program in Chemical and Biological Sciences The Scripps Research Institute La Jolla CA USA. Department of Molecular Biology Princeton University Princeton NJ USA. Department of Chemistry The Scripps Research Institute La Jolla CA USA. ahbadran@scripps.edu. Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA USA. ahbadran@scripps.edu.

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An adapted cardioprotective diet with or without phytosterol and/or krill oil supplement in familial hypercholesterolemia: A pilot study protocol

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Clinical Nutrition Open Science 2024年 54卷 127-139页

作者： de Abreu-Silva, Erlon Oliveira Machado, Rachel Helena Vieira dos Santos, Bianca Rodrigues Kojima, Flávia Soares Santos, Renato Hideo Nakagawa Murizine, Gabriela Souza Homsi, Jordana Rosa Negrelli, Karina Leal Barbante, Letícia Galvão de Barros e Silva, Pedro G.M. de Lima, Andressa Gusmão Tramujas, Lucas Bersch-Ferreira, Ângela Cristine Carvalho, Adriana Bastos de Oliveira, Thaís Martins Izar, Maria Cristina Sampaio, Geni Rodrigues Damasceno, Nágila Raquel Teixeira Rogero, Marcelo Macedo da Silva Torres, Elizabeth Aparecida Ferraz Costa, Rosana Perim de Souza Mota, Luís Gustavo Krey, Julia Pinheiro da Silva, Lucas Ribeiro de Luca, Patrícia Vieira Amaral, Cristiane Kovacs de Oliveira, Patricia Rodrigues da Silva, Renata Alves Moreira, Priscila dos Santos, Elisa Maia de Melo, Rodrigo Morel Vieira Lima, Eduardo Gomes de Luca, André Heck, Thiago Gomes Carvalho, Ana Paula Perillo Ferreira Garofallo, Silvia Bueno Cavalcanti, Alexandre Biasi Marcadenti, Aline Hcor Research Institute SP São Paulo Brazil Division of Health Care Sciences Dresden International University Dresden Germany Department of Education and Research BP - A Beneficência Portuguesa de São Paulo SP São Paulo Brazil Carlos Chagas Filho Biophysics Institute Federal University of Rio de Janeiro RJ Rio de Janeiro Brazil National Institute of Cardiology RJ Rio de Janeiro Brazil Graduate Program in Genetics and Molecular Biology Federal University of Rio Grande do Sul RS Porto Alegre Brazil Paulista School of Medicine Federal University of São Paulo SP São Paulo Brazil Department of Nutrition School of Public Health University of São Paulo SP São Paulo Brazil Hcor Outpatient Nutrition Service SP São Paulo Brazil Hcor Nutrition Service SP São Paulo Brazil Brazilian Association of Familial Hypercholesterolemia SP São Paulo Brazil Dante Pazzanese Institute of Cardiology SP São Paulo Brazil Graduate Program in Cardiovascular Sciences (Professional Master's Degree) National Institute of Cardiology RJ Rio de Janeiro Brazil Graduate Program in Medicine and Health Federal University of Bahia BA Salvador Brazil Hospital Ana Nery BA Salvador Brazil Atherosclerosis Clinical Unit Hospital das Clínicas Heart Institute School of Medicine University of São Paulo SP São Paulo Brazil Dasa Cardiology Unit (Hospital 9 de Julho) SP São Paulo Brazil Clinical Research Center Hospital São José SC Criciúma Brazil Graduate Program in Integral Health Care and Graduate Program in Mathematical and Computational Modeling Regional University of the Northwest of the State of Rio Grande do Sul (UNIJUÍ) RS Ijuí Brazil Health and Nutrition Research Improvement Group /Clinical Hospital Federal University of Goiás GO Goiânia Brazil Feevale University RS Novo Hamburgo Brazil Graduate Program in Health Sciences (Cardiology) Rio Grande do Sul Cardiology Institute/University Foundation of Cardiology RS Porto Alegre Brazil Graduate Program in Epidemiology University

Background and aims: A healthy diet is one of the pillars of familial hypercholesterolemia (FH) treatment. However, the best dietary pattern and indication for specific supplementation have not been established. Our aim is to conduct a pilot study to assess the effect of an adapted cardioprotective diet with or without phytosterol and/or krill oil supplement in participants with a probable or definitive diagnosis of FH, treated with moderate/high potency statins. Methods: A national, multicenter, factorial, and parallel placebo-controlled randomized clinical trial with a superiority design and 1:1:1:1 allocation rate will be conducted. The participants will undergo whole exome sequencing and be allocated into four treatment groups: 1) a cardioprotective diet adapted for FH (DICA-FH) + phytosterol placebo + krill oil placebo;2) DICA-FH + phytosterol 2 g/day + krill oil placebo;3) DICA-FH + phytosterol placebo + krill oil 2 g/day;or 4) DICA-FH + phytosterol 2 g/day + krill oil 2 g/day. The primary outcomes will be low-density lipoprotein (LDL)-cholesterol and lipoprotein (a) levels and adherence to treatment after a 120-day follow-up. LDL- and high-density lipoprotein (HDL)-cholesterol subclasses, untargeted lipidomics analysis, adverse events, and protocol implementation components will also be assessed. Results: A total of 58 participants were enrolled between May–August 2023. After the end of the follow-up period, the efficacy and feasibility results of this pilot study will form the basis of the design of a large-scale randomized clinical trial. Conclusions: This study's overall goal is to recommend dietary treatment strategies in the context of FH. © 2024 The Author(s)

关键词： Diet Fatty acids Healthy Hypercholesterolemia Omega-3 Phytosterols

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Restraint Validation of Biomolecular Structures Determined By NMR in the Protein Data Bank

SSRN

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SSRN 2023年

作者： Baskaran, Kumaran Ploskon, Eliza Tejero, Roberto Yokochi, Masashi Harrus, Deborah Liang, Yuhe Peisach, Ezra Persikova, Irina Ramelot, Theresa A. Sekharan, Monica Tolchard, James Westbrook, John D. Bardiaux, Benjamin Schwieters, Charles D. Patwardnhan, Ardan Venankar, Sameer Burley, Stephen K. Kurisu, Genji Hoch, Jeffrey C. Montelione, Gaetano T. Vuister, Geerten W. Young, Jasmine Y. Biological Magnetic Resonance Data Bank Department of Molecular Biology and Biophysics UConn Health FarmingtonCT06030 United States Department of Molecular and Cell Biology Leicester Institute of Structural and Chemical Biology University of Leicester LeicesterLE1 7RH United Kingdom Department of Chemistry and Chemical Biology Protein Data Bank Japan Institute for Protein Research Osaka University Osaka Suita565-0871 Japan Protein Data Bank Japan Protein Research Foundation Osaka Minoh562-8686 Japan Protein Data Bank in Europe EMBL-EBI Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Research Collaboratory for Structural Bioinformatics Protein Data Bank Institute for Quantitative Biomedicine Rutgers The State University of New Jersey PiscatawayNJ08854 United States Dept of Chemistry and Chemical Biology Center for Biotechnology and Interdisciplinary Sciences Rensselaer Polytechnic Institute TroyNY12180 United States Department of Structural Biology and Chemistry Institut Pasteur Université Paris Cité CNRS UMR3528 Paris75015 France Computational Biomolecular Magnetic Resonance Core National Institute of Diabetes and Digestive and Kidney Diseases BethesdaMD20892 United States The Electron Microscopy Data Bank EMBL-EBI Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Research Collaboratory for Structural Bioinformatics Protein Data Bank San Diego Supercomputer Center University of California La Jolla CA United States Institute for Quantitative Biomedicine Rutgers The State University of New Jersey PiscatawayNJ08854 United States Cancer Institute of New Jersey Rutgers The State University of New Jersey New BrunswickNJ08901 United States Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey PiscatawayNJ08854 United States

Biomolecular structure analysis from experimental NMR generally relies on empirical (residual dipolar couplings, scalar couplings, paramagnetic relaxation enhancements, nuclear Overhauser effects) data and derived geometrical restraints (distance, dihedral angle). A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing establishment of uniform methods of model-vs-data structure validation and limiting interoperability between restraint-based structure modeling programs. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data harvesting system. The resulting wwPDB Restraint Violation Report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints. © 2023, The Authors. All rights reserved.

关键词： Chemical shift

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RETRACTION: Orphan receptor ligand discovery by pickpocketing pharmacological neighbors (Retraction of Vol 13, Pg 235, 2017)

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NATURE CHEMICAL biology 2021年第4期17卷 501-501页

作者： Ngo, Tony Ilatovskiy, Andrey V. Stewart, Alastair G. Coleman, James L. J. McRobb, Fiona M. Riek, R. Peter Graham, Robert M. Abagyan, Ruben Kufareva, Irina Smith, Nicola J. Molecular Cardiology and Biophysics Division Victor Chang Cardiac Research Institute Darlinghurst New South Wales Australia St Vincent’s Clinical School University of New South Wales Darlinghurst New South Wales Australia Molecular Structural and Computational Biology Division Victor Chang Cardiac Research Institute Darlinghurst New South Wales Australia Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla California USA

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Efficient conversion of low-concentration nitrate sources into ammonia on a Ru-dispersed Cu nanowire electrocatalyst

Efficient conversion of low-concentration nitrate sources in...

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2023 AIChE Annual Meeting

作者： Chen, Feng-Yang Wu, Zhen-Yu Gupta, Srishti Rivera, Daniel J. Lambeets, Sten V. Pecaut, Stephanie Kim, Jung Yoon Timothy Zhu, Peng Finfrock, Y. Zou Meira, Debora Motta King, Graham Gao, Guanhui Xu, Wenqian Cullen, David A. Zhou, Hua Han, Yimo Perea, Daniel E. Muhich, Christopher L. Wang, Haotian Department of Chemical and Biomolecular Engineering Rice University HoustonTX United States School for Engineering of Matter Transport & Energy Chemical Engineering Program Arizona State University TempeAZ United States Physical and Computational Sciences Directorate Pacific Northwest National Laboratory RichlandWA United States Structural Biology Center X-ray Science Division Argonne National Laboratory LemontIL United States Canadian Light Source SaskatoonSK Canada Electron Microscope Center Department of Materials Science and NanoEngineering Rice University HoustonTX United States Advanced Photon Source Argonne National Laboratory LemontIL United States Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak RidgeTN United States Department of Materials Science and NanoEngineering Rice University HoustonTX United States Environmental Molecular Sciences Laboratory Earth and Biological Sciences Directorate Pacific Northwest National Laboratory RichlandWA United States School for Engineering of Matter Transport & Energy Materials Science & Engineering Program Arizona State University TempeAZ United States Department of Chemistry Rice University HoustonTX United States

Electrochemically converting nitrate ions, a widely distributed nitrogen source in industrial wastewater and polluted groundwater, into ammonia represents a sustainable route for both wastewater treatment and ammonia generation. However, it is currently hindered by low catalytic activities, especially under low nitrate concentrations. Here we report a high-performance Ru-dispersed Cu nanowire catalyst that delivers an industrial-relevant nitrate reduction current of 1 A cm-2 while maintaining a high NH3 Faradaic efficiency of 93%. More importantly, this high nitrate-reduction catalytic activity enables over a 99% nitrate conversion into ammonia, from an industrial wastewater level of 2, 000 ppm to a drinkable water level 4Cl and liquid NH3 solution products, which suggests a practical approach to convert wastewater nitrate into valuable ammonia products. Density functional theory calculations reveal that the highly dispersed Ru atoms provide active nitrate reduction sites and the surrounding Cu sites can suppress the main side reaction, the hydrogen evolution reaction. © The Author(s), under exclusive licence to Springer Nature Limited 2022.

关键词： Ammonia

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Advances to tackle backbone flexibility in protein docking

arXiv

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arXiv 2020年

作者： Harmalkar, Ameya Gray, Jeffrey J. Department of Chemical and Biomolecular Engineering Johns Hopkins University BaltimoreMD United States Program in Molecular Biophysics Institute for Nanobiotechnology Center for Computational Biology Johns Hopkins University BaltimoreMD United States

computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were submitted in less than 20% of the "difficult" targets (with significant backbone change or uncertainty). Here, we describe recent developments in protein-protein docking and highlight advances that tackle backbone flexibility. In molecular dynamics and Monte Carlo approaches, enhanced sampling techniques have reduced time-scale limitations. Internal coordinate formulations can now capture realistic motions of monomers and complexes using harmonic dynamics. And machine learning approaches adaptively guide docking trajectories or generate novel binding site predictions from deep neural networks trained on protein interfaces. These tools poise the field to break through the longstanding challenge of correctly predicting complex structures with significant conformational change. Copyright © 2020, The Authors. All rights reserved.

关键词： Deep neural networks

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OpenMM 8: molecular Dynamics Simulation with Machine Learning Potentials

arXiv

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arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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Genome and clonal hematopoiesis stability contrasts with immune,cfDNA,mitochondrial,and telomere length changes during short duration spaceflight

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Precision Clinical Medicine 2024年第1期7卷 1-13页

作者： J.Sebastian Garcia-Medina Karolina Sienkiewicz S.Anand Narayanan Eliah G.Overbey Kirill Grigorev Krista A.Ryon Marissa Burke Jacqueline Proszynski Braden Tierney Caleb M.Schmidt Nuria Mencia-Trinchant Remi Klotz Veronica Ortiz Jonathan Foox Christopher Chin Deena Najjar Irina Matei Irenaeus Chan Carlos Cruchaga Ashley Kleinman JangKeun Kim Alexander Lucaci Conor Loy Omary Mzava Iwijn De Vlaminck Anvita Singaraju Lynn E.Taylor Julian C.Schmidt Michael A.Schmidt Kelly Blease Juan Moreno Andrew Boddicker Junhua Zhao Bryan Lajoie Andrew Altomare Semyon Kruglyak Shawn Levy Min Yu Duane C.Hassane Susan M.Bailey Kelly Bolton Jaime Mateus Christopher E.Mason Department of Physiology and Biophysics Weill Cornell MedicineCornell UniversityNew YorkNY 10021USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell MedicineNew YorkNY 10021USA Department of Immunology Weill Cornell MedicineCornell UniversityNew YorkNY 10021USA Department of Stem Cell Biology and Regenerative Medicine Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90033USA Space Exploration Technologies Corporation HawthomeCA 90250USA Sovaris Aerospace BoulderCO 80302USA Advanced Pattern Analysis&Human Performance Group BoulderCO 80302USA Children's Cancer and Blood Foundation Laboratories Departments of Pediatrics and Cell and Developmental BiologyDrukier Institute for Children's HealthMeyer Cancer CenterWeill Cornell MedicineNew YorkNY 10021USA Meyer Cancer Center Weill Cornell MedicineNew YorkNY 10065USA Department of Nutrition and Integrative Physiology Florida State UniversityTallahasseeFL 32306USA Department of Systems Engineering Colorado State UniversityFort CollinsCO 80523USA Element Biosciences San DiegoCA 10055USA Department of Environmental and Radiological Health Sciences Colorado State UniversityFort CollinsCO 80523USA Cell and Molecular Biology Program Colorado State UniversityFort CollinsCO 80523USA BioAstra Inc New YorkNYUSA Washington University St Louis Oncology Division St.LouisMO 63100USA Meinig School of Biomedical Engineering Cornell UniversityIthacaNY 14853USA The Feil Family Brain and Mind Research Institute Weill Cornell MedicineNY 10021USA WorldQuant Initiative for Quantitative Prediction Weill Cornell MedicineNew YorkNY 10021USA

Background The Inspiration4(I4)mission,the first all-civilian orbital flight mission,investigated the physiological effects of short-duration spaceflight through a multi-omic *** advances,there remains much to learn about human adaptation to spaceflight's unique challenges,including microgravity,immune system perturbations,and radiation *** To provide a detailed genetics analysis of the mission,we collected dried blood spots pre-,during,and post-flight for DNA *** length was measured by quantitative PCR,while whole genome and cfDNA sequencing provided insight into genomic stability and immune adaptations.A robust bioinformatic pipeline was used for data analysis,including variant calling to assess mutational *** Telomere elongation occurred during spaceflight and shortened after return to ***-free DNA analysis revealed increased immune cell signatures *** significant clonal hematopoiesis of indeterminate potential(CHIP)or whole-genome instability was *** long-term gene expression changes across immune cells suggested cellular adaptations to the space environment persisting months *** Our findings provide valuable insights into the physiological consequences of short-duration spaceflight,with telomere dynamics and immune cell gene expression adapting to spaceflight and persisting after return to *** sequencing data will serve as a reference point for studying the early development of CHIP in astronauts,an understudied phenomenon as previous studies have focused on career *** study will serve as a reference point for future commercial and non-commercial spaceflight,low Earth orbit(LEO)missions,and deep-space exploration.

关键词： genomes clonal hematopoiesis stability immune mitochondria ribosomes spaceflight

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Towards Autonomous Synchrotron Fourier Transform Infrared Microscopy

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Microscopy and Microanalysis 2024年第SUPPLEMENT_1期30卷

作者： Zwart, Petrus Tas, Neslihan Noack, Marcus Holman, HoiYing Berkeley Synchrotron Infrared Structural Biology Program Lawrence Berkeley National Laboratory Berkeley California USA Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory Berkeley California USA Center for Advanced Mathematics in Energy Research Applications Lawrence Berkeley National Laboratory Berkeley California USA Climate and Ecosystem Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA Applied Mathematics & Computational Research Lawrence Berkeley National Laboratory Berkeley California USA

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