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Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor

细胞研究（英文版） 2021年第5期31卷 593-596页

作者： Youwen Zhuang Brian Krumm Huibing Zhang X.Edward Zhou Yue Wang Xi-Ping Huang Yongfeng Liu Xi Cheng Yi Jiang Hualiang Jiang Cheng Zhang Wei Yi Bryan L.Roth Yan Zhang H.Eric Xu The CAS Key Laboratory of Receptor Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beijing 100049China Department of Pharmacology University of North Carolina at Chapel HillChapel HillNC 27599-7365USA Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital Zhejiang University School of MedicineHangzhouZhejiang 310058China MOE Frontier Science Center for Brain Research and Brain-Machine Integration Zhejiang University School of MedicineHangzhouZhejiang 310058China Center for Cancer and Cell Biology Program for Structural BiologyVan Andel Research InstituteGrand Rapids MIUSA State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China Department of Pharmacology and Chemical Biology School of MedicineUniversity of PittsburghPittsburghPA 15213USA Key Laboratory of Molecular Target & Clinical Pharmacology and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical SciencesGuangzhou Medical UniversityGuangzhouGuangdong 511436China Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital Zhejiang University School of MedicineHangzhouZhejiang 310058China MOE Frontier Science Center for Brain Research and Brain-Machine Integration Zhejiang University School of MedicineHangzhouZhejiang 310058China Liangzhu Laboratory Zhejiang University Medical CenterHangzhouZhejiang 311121China

Dear Editor,Dopamine acts as an essential neurotransmitter whose signal-ing is conducted through five G protein-coupled receptors(GPCRs),dopamine D1 to D5 receptors (DRD1-DRD5).1 The D1-like receptors,comprising DRD1 and DRD5,primarily couple to the Gs family of G proteins to activate adenylyl cyclase and induce cAMP ***1 is the most abundantly expressed dopamine receptor in the CNS.1 It is the central receptor mediating excitatory dopamine signaling in multiple dopaminer-gic *** of DRD1 signaling has been directly linked to Parkinson's disease (PD),schizophrenia,and drug abuse.1,2 Due to its fundamental functions in human diseases,DRD1 has long been the subject of intensive drug development efforts toward the treatment of neuropsychiatric diseases.3 A majority of DRD1 agonists,including the SKF compounds,targets the orthosteric pocket of DRD1,but none has passed clinical trials for neuropsychiatric symptoms to date.3

关键词： Cryoelectron microscopy Single-molecule biophysics

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Gain-of-Function Variant ***2555Arg of von Willebrand Factor Increases Aggregate Size through Altering Stem Dynamics

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Thrombosis and Haemostasis 2021年第2期122卷 226-239页

作者： Volker Huck Po-Chia Chen Emma-Ruoqi Xu Alexander Tischer Ulrike Klemm Camilo Aponte-Santamaría Christian Mess Tobias Obser Fabian Kutzki Gesa König Cécile V. Denis Frauke Gräter Matthias Wilmanns Matthew Auton Stefan W. Schneider Reinhard Schneppenheim Janosch Hennig Maria A. Brehm Department of Dermatology and Venereology Center for Internal Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany Experimental Dermatology Medical Faculty Mannheim Heidelberg University Mannheim Germany Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany European Molecular Biology Laboratory Hamburg Unit Hamburg Germany Division of Hematology Mayo Clinic Rochester Minnesota United States Department of Pediatric Hematology and Oncology University Medical Center Hamburg-Eppendorf Hamburg Germany Max Planck Tandem Group in Computational Biophysics University of los Andes Bogotá Colombia Interdisciplinary Center for Scientific Computing Heidelberg University Heidelberg Germany Molecular Biomechanics Group Heidelberg Institute for Theoretical Studies Heidelberg Germany Institute of Physical Chemistry Karlsruhe Institute of Technology Karlsruhe Germany Laboratory of Hemostasis Inflammation and Thrombosis Institut National de la Santé et de la Recherche Médicale UMR_1176 Université Paris-Saclay Le Kremlin-Bicêtre France University Medical Center Hamburg-Eppendorf Hamburg Germany

The multimeric plasma glycoprotein (GP) von Willebrand factor (VWF) is best known for recruiting platelets to sites of injury during primary hemostasis. Generally, mutations in the

关键词： von Willebrand factor hypercoagulability GPIIb/IIIa

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Novel neutralizing monoclonal antibodies protect rodents against lethal filovirus challenges

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Trials in Vaccinology 2014年第1期3卷 89-94页

作者： Marceau, Caleb D. Negi, Surendra S. Hernandez, Humberto Callison, Julie Marzi, Andrea Borisevich, Viktoriya Braun, Werner Berry, Jody Feldmann, Heinz Rockx, Barry Laboratory of Virology Division of Intramural Research NIAID Hamilton MT United States National Institutes of Health Undergraduate Scholarship Program (NIH-UGSP) United States Department of Pathology University of Texas Medical Branch Galveston TX 77555-0610 301 University Boulevard United States Department of Microbiology and Immunology University of Texas Medical Branch Galveston TX United States Sealy Center for Vaccine Development University of Texas Medical Branch Galveston TX United States Institute for Human Infections and Immunity University of Texas Medical Branch Galveston TX United States Sealy Center for Structural Biology and Molecular Biophysics University of Texas Medical Branch Galveston TX United States BD Biosciences San Diego CA United States Department of Microbiology and Immunology Stanford University United States

Filoviruses are the causative agents of lethal hemorrhagic fever in human and non-human primates (NHP). The family of Filoviridae is composed of three genera, Ebolavirus, Marburgvirus and Cuevavirus. There are currently no approved vaccines or antiviral therapeutics for the treatment of filovirus infections in humans. Passive transfer of neutralizing antibodies targeting the Ebola virus (EBOV) glycoprotein (GP) has proven effective in protecting mice, guinea pigs and NHP from lethal challenges with EBOV. In this study, we generated two neutralizing monoclonal antibodies (MAbs), termed S9 and M4 that recognize the GP of EBOV or multiple strains of Marburg virus (MARV), respectively. We characterized the putative binding site of S9 as a linear epitope on the glycan cap of the GP₁ subunit of the EBOV-GP. The M4 antibody recognizes an unknown conformational epitope on MARV-GP. Additionally, we demonstrated the post-exposure protection potential of these antibodies in both the mouse and guinea pig models of filovirus infection. These data indicate that MAbs S9 and M4 would be good candidates for inclusion in an antibody cocktail for the treatment of filovirus infections. © 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license.

关键词： Animal model Filovirus Neutralizing antibody Prophylaxis

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qlty: handling large tensors in scientific imaging deep-learning workflows

arXiv

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arXiv 2024年

作者： Zwart, Petrus H. Center for Advanced Mathematics in Energy Research Applications Lawrence Berkeley National Laboratory 1 Cyclotron Road BerkeleyCA94720 United States Berkeley Synchrotron Infrared Structural Biology program Lawrence Berkeley National Laboratory 1 Cyclotron Road BerkeleyCA94720 United States Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Road BerkeleyCA94720 United States

In scientific imaging, deep learning has become a pivotal tool for image analytics. However, handling large volumetric datasets, which often exceed the memory capacity of standard GPUs, require special attention when subjected to deep learning efforts. This paper introduces qlty, a toolkit designed to address these challenges through tensor management techniques. qlty offers robust methods for subsampling, cleaning, and stitching of large-scale spatial data, enabling effective training and inference even in resource-limited environments. Copyright © 2024, The Authors. All rights reserved.

关键词： Contrastive Learning

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Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

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molecular Systems biology 2008年第1期4卷 198-198页

作者： Kunin, Victor Raes, Jeroen Harris, J. Kirk Spear, John R. Walker, Jeffrey J. Ivanova, Natalia Von Mering, Christian Bebout, Brad M. Pace, Norman R. Bork, Peer Hugenholtz, Philip Microbial Ecology Program DOE Joint Genome Institute Walnut Creek CA United States Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany Department of Pediatrics University of Colorado Denver Aurora CO United States Division of Environmental Science and Engineering Colorado School of Mines Golden CO United States Department of Molecular Cellular and Developmental Biology University of Colorado Boulder CO United States Genome Biology Program DOE Joint Genome Institute Walnut Creek CA United States Institute of Molecular Biology Swiss Institute of Bioinformatics University of Zurich Zurich Switzerland Microbial Ecology/Biogeochemistry Research Laboratory Exobiology Branch NASA Ames Research Center Moffett Field CA United States Microbial Ecology Program DOE Joint Genome Institute Walnut Creek CA 94598 2800 Mitchell Drive United States

To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near-identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino-acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community. © 2008 EMBO and Nature Publishing Group All rights reserved.

关键词： Fine-scale Hypersalinity Metagenomics Microbial ecology Salt-in

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Visualizing cortical blood perfusion after photothrombotic stroke in vivo by needle-shaped beam optical coherence tomography angiography

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PhotoniX 2024年第1期5卷 605-621页

作者： Xiangyu Guo Jingjing Zhao Liqun Sun Varun Gupta Lin Du Komal Sharma Aidan Van Vleck Kaitlyn Liang Liangcai Cao Lingjie Kong Yuanmu Yang Yong Huang Adam de la Zerda Guofan Jin State Key Laboratory of Precision Measurement Technology and Instruments Department of Precision InstrumentTsinghua UniversityBeijing 100084China Department of Structural Biology Stanford University School of MedicineStanford UniversityStanfordCA 94305USA Department of Neurosurgery Stanford University School of MedicineStanford UniversityStanfordCA 94305USA Department of Radiology Stanford University School of MedicineStanford UniversityStanfordCA 94305USA Department of Electrical Engineering and Computer Sciences University of CaliforniaBerkeley 94720USA School of Optics and Photonics Beijing Institute of TechnologyNo.5 South Zhongguancun StreetHaidianBeijing 100081China Biophysics Program Molecular Imaging Programand Bio-X Program at Stanford UniversityStanfordCA 94305USA Chan Zuckerberg Biohub San FranciscoCA 94110USA Institute of Medical Equipment Science and Engineering Huazhong University of Science and TechnologyWuhan 430074China

Optical imaging techniques provide low-cost,non-radiative images with high spatiotemporal resolution,making them advantageous for long-term dynamic observation of blood perfusion in stroke research and other brain studies compared to non-optical ***,high-resolution imaging in optical microscopy fundamentally requires a tight optical focus,and thus a limited depth of field(DOF).Consequently,large-scale,non-stitched,high-resolution images of curved surfaces,like brains,are difficult to acquire without z-axis *** overcome this limitation,we developed a needle-shaped beam optical coherence tomography angiography(NB-OCTA)system,and for the first time,achieved a volumetric resolution of less than 8μm in a non-stitched volume space of 6.4 mm×4 mm×620μm in *** system captures the distribution of blood vessels at 3.4-times larger depths than normal OCTA equipped with a Gaussian beam(GB-OCTA).We then employed NB-OCTA to perform long-term observation of cortical blood perfusion after stroke in vivo,and quantitatively analyzed the vessel area density(VAD)and the diameters of representative vessels in different regions over 10 days,revealing different spatiotemporal dynamics in the acute,sub-acute and chronic phase of post-ischemic *** from our NB-OCTA,we revealed that the recovery process is not only the result of spontaneous reperfusion,but also the formation of new *** study provides visual and mechanistic insights into strokes and helps to deepen our understanding of the spontaneous response of brain after stroke.

关键词： Optical coherence tomography angiography Diffractive optical elements Needle-shaped beam Brain imaging Stroke Cortical blood perfusion

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structural insights into binding specificity, efficacy and bias of a β2AR partial agonist (vol 14, pg 1059, 2018)

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NATURE CHEMICAL biology 2019年第2期15卷 205-205页

作者： Masureel, Matthieu Zou, Yaozhong Picard, Louis-Philippe van der Westhuizen, Emma Mahoney, Jacob P. Rodrigues, Joao P. G. L. M. Mildorf, Thomas J. Dror, Ron O. Shaw, David E. Bouvier, Michel Pardon, Els Steyaert, Jan Sunahara, Roger K. Weis, William I. Zhang, Cheng Kobilka, Brian K. Department of Molecular and Cellular Physiology Stanford University School of Medicine Stanford USA Geneus Technologies Ltd Chengdu People’s Republic of China Department of Biochemistry Institute for Research in Immunology and Cancer Université de Montreal Montreal Québec Canada Monash Institute for Pharmaceutical Sciences Monash University Victoria Australia Department of Pharmacology University of Michigan Ann Arbor USA Department of Computer Science Stanford University Stanford USA Department of Structural Biology Stanford University Stanford USA D. E. Shaw Research New York USA Dropbox New York USA Department of Computer Science and Institute for Computational and Mathematical Engineering Stanford University Stanford USA Department of Biochemistry and Molecular Biophysics Columbia University New York USA Structural Biology Brussels Vrije Universiteit Brussel Brussels Belgium Structural Biology Research Center VIB Brussels Belgium Department of Pharmacology University of California San Diego School of Medicine La Jolla USA Department of Pharmacology and Chemical Biology University of Pittsburgh School of Medicine Pittsburgh USA

In the version of this paper originally published, the structure for epinephrine shown in Figure 1a was redrawn with an extra carbon. The structure has been replaced in the HTML and PDF versions of the article. The or... 详细信息

关键词： Statistical Biases bias(electronics) Bias Specificity partial agonist

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GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

arXiv

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arXiv 2017年

作者： Pryor, Alan Yang, Yongsoo Rana, Arjun Gallagher-Jones, Marcus Zhou, Jihan Lo, Yuan Hung Melinte, Georgian Chiu, Wah Rodriguez, Jose A. Miao, Jianwei Department of Physics and Astronomy California NanoSystems Institute University of California Los AngelesCA90095 United States Department of Chemistry & Biochemistry UCLA-DOE Institute of Genomics and Proteomics Los AngelesCA90095-1570 United States Department of Bioengineering University of California Los AngelesCA90095 United States Institut de Physique et Chimie des Matériaux de Strasbourg CNRS-Université de Strasbourg 23 rue du Loess Cedex 08 Strasbourg67037 France Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine HoustonTX77030 United States

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. In many scientific applications, however, the number of projections that can be measured is limited due to geometric constraints, tolerable radiation dose and/or acquisition speed. Thus it becomes an important problem to obtain the best-possible reconstruction from a limited number of projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between real and reciprocal space, GENFIRE searches for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques by numerical simulations, and by experimentally by reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines. Copyright © 2017, The Authors. All rights reserved.

关键词： Tomography

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Identifying topologically associating domains using differential kernels

arXiv

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arXiv 2023年

作者： Maisuradze, Luka King, Megan C. Surovtsev, Ivan V. Mochrie, Simon G.J. Shattuck, Mark D. O’Hern, Corey S. Department of Molecular Biophysics and Biochemistry Yale University New HavenCT United States Department of Cell Biology Yale School of Medicine New HavenCT United States Department of Physics Yale University New HavenCT United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT United States

Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin. Hi-C maps can be represented as a symmetric matrix Aij, where each element represents the average contact probability or number of contacts between chromatin loci i and j. Previous studies have detected topologically associating domains (TADs), or self-interacting regions in Aij within which the contact probability is greater than that outside the region. Many algorithms have been developed to identify TADs within Hi-C maps. However, most TAD identification algorithms are unable to identify nested or overlapping TADs and for a given Hi-C map there is significant variation in the location and number of TADs identified by different methods. We develop a novel method to identify TADs, KerTAD, using a kernel-based technique from computer vision and image processing that is able to accurately identify nested and overlapping TADs. We benchmark this method against state-of-the-art TAD identification methods on both synthetic and experimental data sets. We find that the new method consistently has higher true positive rates (TPR) and lower false discovery rates (FDR) than all tested methods for both synthetic and manually annotated experimental Hi-C maps. The TPR for KerTAD is also largely insensitive to increasing noise and sparsity, in contrast to the other methods. We also find that KerTAD is consistent in the number and size of TADs identified across replicate experimental Hi-C maps for several organisms. Thus, KerTAD will improve automated TAD identification and enable researchers to better correlate changes in TADs to biological phenomena, such as enhancer-promoter interactions and disease states. © 2023, CC BY.

关键词： Topology

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Single-image example-based superresolution of hyperpolarized 13C images

arXiv

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arXiv 2023年

作者： Deh, Kofi Coffee, Elizabeth Zhang, Guannan Kim, Nathaniel Miloushev, Vesselin Keshari, Kayvan R. Department of Radiology Memorial Sloan Kettering Cancer Center New York CityNY United States Department of Neurology Memorial Sloan Kettering Cancer Center New York CityNY United States Department of Physiology & Biophysics Weill Cornell Graduate School New York CityNY United States Department of Biochemistry & Structural Biology Weill Cornell Graduate School NYCNY United States Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center NYCNY United States

The transient signal available for hyperpolarized (HP) 13C imaging limits the image spatial resolution. This paper demonstrates a method of increasing spatial resolution by post-processing the HP 13C metabolic map using a corresponding anatomic image as a high-resolution example. The proposed method is tested with a Shepp-Logan digital phantom and for an MR image of a tumor in a mouse brain acquired at 3 Tesla using 13C Chemical Shift Imaging. The results are compared to the results of standard image rescaling methods using peak-signal-to-noise ratio and structural similarity index (SSIM) image quality metrics. In vivo, the method reduced blur resulting in a better match between the metabolite biodistribution and the anatomy. It is concluded that the image quality of hyperpolarized 13C MRI in vivo images can be improved with single image superresolution using the anatomic image as an example. © 2023, CC0.

关键词： Magnetic resonance imaging

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