Výsledky vyhľadávania - "protein dynamics"

Addressing structural heterogeneity in real-time tracking of protein dynamics triggered by caged compounds

Autori: Magkakis, Konstantinos Orädd, Fredrik Pett, Christian a ďalší

Zdroj: Journal of Molecular Biology. 437(24)

Predmety: adenylate kinase, ensemble optimization, genetic algorithm, protein dynamics, time-resolved X-ray solution scattering

Popis súboru: electronic

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-245931
https://doi.org/10.1016/j.jmb.2025.169476

Dynamic networks connect the USP14 active site region with the proteasome interaction surface

Autori: Salomonsson, Johannes Sjöstrand, Linda Eskilson, Arvid a ďalší

Zdroj: Protein Science. 34(4)

Predmety: allostery, deubiquitinases (DUBs), NMR spectroscopy, protein dynamics, ubiquitin specific proteases (USP), ubiquitin-proteasome system (UPS)

Popis súboru: electronic

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-212536
https://liu.diva-portal.org/smash/get/diva2:1947241/FULLTEXT01.pdf

SHP-1 Variants Broaden the Understanding of pH-Dependent Activities in Protein Tyrosine Phosphatases

Autori: Shen, Ruidan Brownless, Alfie-Louise R. Alansson, Nikolas a ďalší

Zdroj: JACS Au. 4(8):2874-2885

Predmety: protein tyrosine phosphatases, enzyme kinetics, protein dynamics, loop dynamics, pH dependency, molecular dynamics simulations

Popis súboru: electronic

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-541968
https://doi.org/10.1021/jacsau.4c00078

Learning how to simulate : Applying machine learning methods to improve molecular dynamics simulations

Autori: Pérez Culubret, Adrià

Prispievatelia: University/Department: Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut

Thesis Advisors: De Fabritiis, Gianni

Zdroj: TDX (Tesis Doctorals en Xarxa)

Predmety: Molecular dynamics, Machine learning, Adaptive sampling, Disordered proteins, Protein dynamics, Dinàmica molecular, Aprenentatge automàtic, Mostreig adaptatiu, Proteïnes desordenades, Dinàmica de proteïnes

Popis súboru: application/pdf

Prístupová URL adresa: http://hdl.handle.net/10803/673392

A Structural and Functional Bioinformatics Study of QTY-designed Retinylidene Proteins

Autori: Pan, Siqi

Zdroj: QRB Discovery, Vol 6 (2025)

Predmety: protein dynamics simulation, QH301-705.5, computational studies on functional properties of biological molecule, bioinformatics, membrane protein structure, Biology (General), GPCRs, TP248.13-248.65, Biotechnology

Prístupová URL adresa: https://doaj.org/article/dacd72c051b548bc807b790304a0493b

Instrumentation and methods for efficient time-resolved X-ray crystallography of biomolecular systems with sub-10 ms time resolution

Autori: John A. Indergaard Kashfia Mahmood Leo Gabriel a ďalší

Zdroj: IUCrJ
IUCrJ, Vol 12, Iss 3, Pp 372-383 (2025)

Predmety: Crystallography, Time Factors, QD901-999, time-resolved crystallography, protein dynamics, time-resolved cryo-em, enzyme mechanism, Muramidase, Crystallography, X-Ray, Research Papers, mix and quench, Synchrotrons

Prístupová URL adresa: https://pubmed.ncbi.nlm.nih.gov/40277177
https://doaj.org/article/f17928a8f1254d5589afbe0c02123ede

Advancing Molecular Simulations: Merging Physical Models, Experiments, and AI to Tackle Multiscale Complexity

Autori: Giorgio Bonollo Gauthier Trèves Denis Komarov a ďalší

Zdroj: J Phys Chem Lett

Predmety: Protein dynamics, Molecular dynamics, Artificial intelligence, Protein–protein interactions, ligand binding, Multiscale modeling

Popis súboru: application/pdf

Prístupová URL adresa: https://pubmed.ncbi.nlm.nih.gov/40179097

Flexibility in PAM recognition expands DNA targeting in xCas9.

Autori: Hossain, Kazi Nierzwicki, Lukasz Orozco, Modesto a ďalší

Predmety: CRISPR-Cas9, RNA, S. pyogenes, entropy, genome editing, molecular biophysics, protein dynamics, protein-DNA, structural biology, DNA, CRISPR-Associated Protein 9, CRISPR-Cas Systems, Gene Editing, Humans

Popis súboru: application/pdf

Prístupová URL adresa: https://escholarship.org/uc/item/2wr0z6pv
https://escholarship.org/content/qt2wr0z6pv/qt2wr0z6pv.pdf

Allosteric Modulation of Pathological Ataxin-3 Aggregation: A Path to Spinocerebellar Ataxia Type-3 Therapies

Autori: Silva, Alexandra Duarte-Silva, Sara Martins, Pedro M a ďalší

Zdroj: bioRxiv

Predmety: 3101 Biochemistry and Cell Biology (for-2020), 31 Biological Sciences (for-2020), Rare Diseases (rcdc), Orphan Drug (rcdc), Neurodegenerative (rcdc), Brain Disorders (rcdc), Neurosciences (rcdc), Aging (rcdc), 5.1 Pharmaceuticals (hrcs-rac), Neurological (hrcs-hc), Amyloid, Molecular therapies, Polyglutamine, Pre-clinical models, Protein dynamics

Popis súboru: application/pdf

Prístupová URL adresa: https://escholarship.org/uc/item/1fp178nx
https://escholarship.org/content/qt1fp178nx/qt1fp178nx.pdf

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

Autori: Srdan Masirevic Jan K. Marzinek Jiquan Liu a ďalší

Zdroj: Scientific Reports, Vol 15, Iss 1, Pp 1-8 (2025)

Predmety: MS2 bacteriophage, Maturation protein, Molecular dynamics simulations, Viral infectivity, Protein dynamics, Capsid stability, Medicine, Science

Popis súboru: electronic resource

Relation: https://doaj.org/toc/2045-2322

Prístupová URL adresa: https://doaj.org/article/90ed3d8c1eec405f8d7b8b8a218cb474

Automated Engineering Protein Dynamics via Loop Grafting: Improving Renilla Luciferase Catalysis

Autori: Planas-Iglesias, Joan Majerova, Marika Pluskal, Daniel a ďalší

Zdroj: ACS Catal
ACS Catalysis

Predmety: loop grafting, protein dynamics, bifunctionalprotein chimeras, Renilla luciferase, enzyme engineering, bioluminescent catalytic activity

Prístupová URL adresa: https://pubmed.ncbi.nlm.nih.gov/40013243

Multimeric protein interaction and complex prediction: Structure, dynamics and function

Autori: Da Lu Shuhong Yu Yixiang Huang a ďalší

Zdroj: Comput Struct Biotechnol J
Computational and Structural Biotechnology Journal, Vol 27, Iss, Pp 1975-1997 (2025)

Predmety: Protein-protein interaction, Protein function, Deep learning, Protein dynamics, Review Article, Protein multimer prediction, TP248.13-248.65, Quality assessment, Biotechnology

Prístupová URL adresa: https://doaj.org/article/a7e95b0dc3b04068b5f304aee6e74645

Riemannian geometry for efficient analysis of protein dynamics data

Autori: Diepeveen, Willem Esteve-Yagüe, Carlos Lellmann, Jan a ďalší

Zdroj: Proceedings of the National Academy of Sciences of the United States of America. 121(33)

Predmety: dimension reduction, interpolation, manifold-valued data, protein dynamics, Riemannian manifold

Popis súboru: print

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-366654
https://doi.org/10.1073/pnas.2318951121

Structural dynamics of human deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)

Autori: Sarre, Ravdna Dobrovolska, Olena Lundström, Patrik a ďalší

Zdroj: Scientific Reports. 14(1)

Predmety: Human dUTPase, Protein dynamics, Multidimensional NMR

Popis súboru: electronic

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-209920
https://liu.diva-portal.org/smash/get/diva2:1914753/FULLTEXT01.pdf

Transient interdomain interactions in free USP14 shape its conformational ensemble

Autori: Salomonsson, Johannes Wallner, Björn Sjöstrand, Linda a ďalší

Zdroj: Protein Science. 33(5)

Predmety: DUB, molecular modeling, NMR, protein dynamics, SAXS

Popis súboru: electronic

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-202471
https://liu.diva-portal.org/smash/get/diva2:1851579/FULLTEXT01.pdf

Automated matching of two-time X-ray photon correlation mans from phase-separating proteins with Cahn-Hilliard-type simulations using auto-encoder networks

Autori: Timmermann, Sonja Starostin, Vladimir Girelli, Anita a ďalší

Zdroj: Journal of applied crystallography. 55:751-757

Predmety: protein dynamics, X-ray photon correlation spectroscopy, XPCS, Cahn-Hilliard, auto-encoders, machine learning

Popis súboru: print

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-209794
https://doi.org/10.1107/S1600576722004435

Tracking Membrane Protein Dynamics in Real Time

Autori: Orädd, Fredrik Andersson, Magnus

Zdroj: Journal of Membrane Biology. 254(1):51-64

Predmety: Membrane protein dynamics, MD simulation, X-ray solution scattering

Popis súboru: electronic

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-179034
https://doi.org/10.1007/s00232-020-00165-8

Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover

Autori: Winter, Samuel D. Jones, Hannah B. L. Rasadean, Dora M. a ďalší

Zdroj: ACS Catalysis. 11(24):14854-14863

Predmety: enzyme, catalysis, protein dynamics, molecular dynamics, temperature dependence, MMRT

Popis súboru: electronic

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-469180
https://doi.org/10.1021/acscatal.1c04679

Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases

Autori: Shen, Ruidan Crean, Rory M. Johnson, Sean J. a ďalší

Zdroj: JACS Au. 1(5):646-659

Predmety: Protein tyrosine phosphatases, Enzyme kinetics, Protein dynamics, Enzyme catalysis, Point mutation, Loop dynamics, pH dependence, Molecular dynamics simulations

Popis súboru: electronic

Prístupová URL adresa: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-446888
https://doi.org/10.1021/jacsau.1c00054

Activity‐Enhancing Mutations in an LmrR‐Based Artificial Metalloenzyme Destabilize the Protein Scaffold and Alter its Conformational Plasticity

Autori: Adil A. Safeer Fabrizio Casilli Wouter Beugelink a ďalší

Zdroj: ChemBioChem. 26

Predmety: nuclear magnetic resonance, artificial metalloenzymes, enzyme design, protein dynamics, biocatalyses

Prístupová URL adresa: https://research.rug.nl/en/publications/b7ecba0e-3e34-4685-bd21-db6a453e7e39
https://doi.org/10.1002/cbic.202500259
https://hdl.handle.net/11370/b7ecba0e-3e34-4685-bd21-db6a453e7e39