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  1. Article: Multi-crystal native-SAD phasing at 5 keV with a helium environment.

    Karasawa, Akira / Andi, Babak / Fuchs, Martin R / Shi, Wuxian / McSweeney, Sean / Hendrickson, Wayne A / Liu, Qun

    IUCrJ

    2022  Volume 9, Issue Pt 6, Page(s) 768–777

    Abstract: ... De ... ...

    Abstract De novo
    Language English
    Publishing date 2022-10-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S205225252200971X
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3.

    Li, Yunfeng / Pustovalova, Yulia / Shi, Wuxian / Gorbatyuk, Oksana / Sreeramulu, Sridhar / Schwalbe, Harald / Hoch, Jeffrey C / Hao, Bing

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 2890

    Abstract: Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known ... ...

    Abstract Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.
    MeSH term(s) Humans ; SARS-CoV-2/metabolism ; Molecular Docking Simulation ; Pandemics ; COVID-19 ; Protein Domains ; Viral Nonstructural Proteins/genetics
    Chemical Substances Viral Nonstructural Proteins
    Language English
    Publishing date 2023-02-18
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-30045-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: On the Rate-Distortion-Perception Function

    Chen, Jun / Yu, Lei / Wang, Jia / Shi, Wuxian / Ge, Yiqun / Tong, Wen

    2022  

    Abstract: Rate-distortion-perception theory generalizes Shannon's rate-distortion theory by introducing a constraint on the perceptual quality of the output. The perception constraint complements the conventional distortion constraint and aims to enforce ... ...

    Abstract Rate-distortion-perception theory generalizes Shannon's rate-distortion theory by introducing a constraint on the perceptual quality of the output. The perception constraint complements the conventional distortion constraint and aims to enforce distribution-level consistencies. In this new theory, the information-theoretic limit is characterized by the rate-distortion-perception function. Although a coding theorem for the rate-distortion-perception function has recently been established, the fundamental nature of the optimal coding schemes remains unclear, especially regarding the role of randomness in encoding and decoding. It is shown in the present work that except for certain extreme cases, the rate-distortion-perception function is achievable by deterministic codes. This paper also clarifies the subtle differences between two notions of perfect perceptual quality and explores some alternative formulations of the perception constraint.
    Keywords Computer Science - Information Theory
    Subject code 003
    Publishing date 2022-04-12
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Online: On Distributed Lossy Coding of Symmetrically Correlated Gaussian Sources

    Zhou, Siyao / Salehkalaibar, Sadaf / Qian, Jingjing / Chen, Jun / Shi, Wuxian / Ge, Yiqun / Tong, Wen

    2022  

    Abstract: A distributed lossy compression network with $L$ encoders and a decoder is considered. Each encoder observes a source and sends a compressed version to the decoder. The decoder produces a joint reconstruction of target signals with the mean squared error ...

    Abstract A distributed lossy compression network with $L$ encoders and a decoder is considered. Each encoder observes a source and sends a compressed version to the decoder. The decoder produces a joint reconstruction of target signals with the mean squared error distortion below a given threshold. It is assumed that the observed sources can be expressed as the sum of target signals and corruptive noises which are independently generated from two symmetric multivariate Gaussian distributions. The minimum compression rate of this network versus the distortion threshold is referred to as the rate-distortion function, for which an explicit lower bound is established by solving a minimization problem. Our lower bound matches the well-known Berger-Tung upper bound for some values of the distortion threshold. The asymptotic gap between the upper and lower bounds is characterized in the large $L$ limit.
    Keywords Computer Science - Information Theory
    Subject code 003
    Publishing date 2022-01-19
    Publishing country us
    Document type Book ; Online
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  5. Article: Synchrotron microcrystal native-SAD phasing at a low energy.

    Guo, Gongrui / Zhu, Ping / Fuchs, Martin R / Shi, Wuxian / Andi, Babak / Gao, Yuan / Hendrickson, Wayne A / McSweeney, Sean / Liu, Qun

    IUCrJ

    2019  Volume 6, Issue Pt 4, Page(s) 532–542

    Abstract: ... De ... ...

    Abstract De novo
    Language English
    Publishing date 2019-05-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252519004536
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Red Emission Carbon Dots Prepared by 1,4-Diaminonaphthalene for Light-Emitting Diode Application and Metal Ion Detection.

    An, Yulong / Lin, Xu / Guo, Zewen / Yin, Qitao / Li, Yan / Zheng, Yunwu / Shi, Zhengjun / Zhang, Wuxian / Liu, Can

    Materials (Basel, Switzerland)

    2021  Volume 14, Issue 16

    Abstract: Carbon dots (CDs), as the most important type of carbon materials, have been widely used in many fields because of their unique fluorescence characteristics and excellent properties of biocompatibility. In previous studies, the fluorescence of CDs was ... ...

    Abstract Carbon dots (CDs), as the most important type of carbon materials, have been widely used in many fields because of their unique fluorescence characteristics and excellent properties of biocompatibility. In previous studies, the fluorescence of CDs was mainly concentrated in the blue and green, whereas the red fluorescence was relatively less. Herein, we prepared efficient red-emitting CDs from 1,4-diaminonaphthalene using solvothermal methods. We discussed the effects of different solvothermal solvents on CDs. The results show that CDs prepared with octane and acetone as reaction media have the best fluorescence properties. The CDs dispersed in different organic solvents exhibited tunable emission across a wide spectrum from 427 nm to 679 nm. We further demonstrated the application of red light-emitting diode (LED) optoelectronics and fluorescence detection of Fe
    Language English
    Publishing date 2021-08-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2487261-1
    ISSN 1996-1944
    ISSN 1996-1944
    DOI 10.3390/ma14164716
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Imaging of Tumor-Associated Vascular Prostate-Specific Membrane Antigen in Woodchuck Model of Hepatocellular Carcinoma.

    Sergeeva, Olga / Zhang, Yifan / Julian, Willian / Sasikumar, Arun / Awadallah, Amad / Kenyon, Jonathan / Shi, Wuxian / Sergeev, Maxim / Huang, Steve / Sexton, Sandra / Iyer, Renuka / Xin, Wei / Avril, Norbert / Chan, Ernest Ricky / Lee, Zhenghong

    Gastro hep advances

    2022  Volume 1, Issue 4, Page(s) 631–639

    Abstract: Background and aims: Radiolabeled short peptide ligands targeting prostate-specific membrane antigen (PSMA) were developed initially for imaging and treatment of prostate cancers. While many nonprostate solid tumors including hepatocellular carcinoma ( ... ...

    Abstract Background and aims: Radiolabeled short peptide ligands targeting prostate-specific membrane antigen (PSMA) were developed initially for imaging and treatment of prostate cancers. While many nonprostate solid tumors including hepatocellular carcinoma (HCC) express little PSMA, their neovasculature expresses a high level of PSMA, which is avid for Gallium-68-labeled PSMA-targeting radio-ligand (
    Methods: Molecular docking was performed with 3 bait PSMA ligands and compared between human and woodchuck PSMA. Initially, PET images were acquired dynamically after intravenously injecting 37 MBq (1.0 mCi) of
    Results: Our preclinical studies confirmed the initial clinical findings of
    Conclusion: This animal model offers a unique opportunity for investigating the biogenesis of tumor-associated vascular PSMA, its functional role(s), and potentials for future treatment strategies targeting tumor vascular PSMA using already developed PSMA-targeting agents.
    Language English
    Publishing date 2022-04-28
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2772-5723
    ISSN (online) 2772-5723
    DOI 10.1016/j.gastha.2022.04.014
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  8. Article ; Online: Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen.

    Wright, Katharine M / DiNapoli, Sarah R / Miller, Michelle S / Aitana Azurmendi, P / Zhao, Xiaowei / Yu, Zhiheng / Chakrabarti, Mayukh / Shi, WuXian / Douglass, Jacqueline / Hwang, Michael S / Hsiue, Emily Han-Chung / Mog, Brian J / Pearlman, Alexander H / Paul, Suman / Konig, Maximilian F / Pardoll, Drew M / Bettegowda, Chetan / Papadopoulos, Nickolas / Kinzler, Kenneth W /
    Vogelstein, Bert / Zhou, Shibin / Gabelli, Sandra B

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 5063

    Abstract: Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides ... ...

    Abstract Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRAS
    MeSH term(s) Proto-Oncogene Proteins p21(ras)/genetics ; Antibodies ; Recognition, Psychology ; Hydrophobic and Hydrophilic Interactions ; HLA-A Antigens/genetics
    Chemical Substances Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; Antibodies ; HLA-A Antigens
    Language English
    Publishing date 2023-08-21
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-40821-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.

    Andi, Babak / Kumaran, Desigan / Kreitler, Dale F / Soares, Alexei S / Keereetaweep, Jantana / Jakoncic, Jean / Lazo, Edwin O / Shi, Wuxian / Fuchs, Martin R / Sweet, Robert M / Shanklin, John / Adams, Paul D / Schmidt, Jurgen G / Head, Martha S / McSweeney, Sean

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 12197

    Abstract: Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to ... ...

    Abstract Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (M
    MeSH term(s) Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Coronavirus 3C Proteases ; Cysteine Endopeptidases/metabolism ; Hepacivirus/metabolism ; Humans ; Molecular Docking Simulation ; Protease Inhibitors/chemistry ; SARS-CoV-2 ; Viral Nonstructural Proteins/genetics
    Chemical Substances Antiviral Agents ; Protease Inhibitors ; Viral Nonstructural Proteins ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2022-07-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-15930-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Serial crystallography with multi-stage merging of thousands of images.

    Soares, Alexei S / Yamada, Yusuke / Jakoncic, Jean / McSweeney, Sean / Sweet, Robert M / Skinner, John / Foadi, James / Fuchs, Martin R / Schneider, Dieter K / Shi, Wuxian / Andi, Babak / Andrews, Lawrence C / Bernstein, Herbert J

    Acta crystallographica. Section F, Structural biology communications

    2022  Volume 78, Issue Pt 7, Page(s) 281–288

    Abstract: KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support ... ...

    Abstract KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences.
    MeSH term(s) Algorithms ; Cluster Analysis ; Crystallography, X-Ray ; Proteins/chemistry ; Software
    Chemical Substances Proteins
    Language English
    Publishing date 2022-07-04
    Publishing country United States
    Document type Journal Article
    ISSN 2053-230X
    ISSN (online) 2053-230X
    DOI 10.1107/S2053230X22006422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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