6svb: Difference between revisions
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The | ==Terahertz irradiated structure of bovine trypsin (odd frames of crystal x40)== | ||
<StructureSection load='6svb' size='340' side='right'caption='[[6svb]], [[Resolution|resolution]] 1.15Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6svb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SVB FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6svb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6svb OCA], [http://pdbe.org/6svb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6svb RCSB], [http://www.ebi.ac.uk/pdbsum/6svb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6svb ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments. | |||
Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.,Gagner VA, Lundholm I, Garcia-Bonete MJ, Rodilla H, Friedman R, Zhaunerchyk V, Bourenkov G, Schneider T, Stake J, Katona G Sci Rep. 2019 Dec 17;9(1):19281. doi: 10.1038/s41598-019-55777-5. PMID:31848402<ref>PMID:31848402</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6svb" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bos taurus]] | |||
[[Category: Large Structures]] | |||
[[Category: Trypsin]] | |||
[[Category: Bourenkov, G]] | |||
[[Category: Friedman, R]] | |||
[[Category: Gagner, V Ahlberg]] | |||
[[Category: Garcia-Bonete, M J]] | |||
[[Category: Katona, G]] | |||
[[Category: Lundholm, I]] | |||
[[Category: Rodilla, H]] | |||
[[Category: Schneider, T]] | |||
[[Category: Stake, J]] | |||
[[Category: Zhaunerchyk, V]] | |||
[[Category: Bovine trypsin]] | |||
[[Category: Hydrolase]] | |||
[[Category: Odd frame]] | |||
[[Category: Terahertz irradiation]] | |||
[[Category: X40]] | |||
Latest revision as of 19:21, 29 January 2020
Terahertz irradiated structure of bovine trypsin (odd frames of crystal x40)Terahertz irradiated structure of bovine trypsin (odd frames of crystal x40)
Structural highlights
Publication Abstract from PubMedLow-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments. Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.,Gagner VA, Lundholm I, Garcia-Bonete MJ, Rodilla H, Friedman R, Zhaunerchyk V, Bourenkov G, Schneider T, Stake J, Katona G Sci Rep. 2019 Dec 17;9(1):19281. doi: 10.1038/s41598-019-55777-5. PMID:31848402[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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