Geometry, Energetics, and Dynamics of Hydrogen Bonds in Proteins:  Structural Information Derived from NMR Scalar Couplings

2006 ◽  
Vol 128 (47) ◽  
pp. 15127-15135 ◽  
Author(s):  
Joerg Gsponer ◽  
Harri Hopearuoho ◽  
Andrea Cavalli ◽  
Christopher M. Dobson ◽  
Michele Vendruscolo
Keyword(s):  
Hydrogen Bonds ◽  
Structural Information ◽  
Scalar Couplings

Detection of Scalar Couplings Across NH···OP and OH···OP Hydrogen Bonds in a Flavoprotein

2000 ◽  
Vol 122 (38) ◽  
pp. 9289-9295 ◽  
Author(s):  
Frank Löhr ◽  
Stephen G. Mayhew ◽  
Heinz Rüterjans
Keyword(s):  
Hydrogen Bonds ◽  
Scalar Couplings

Direct Observation of Intramolecular Hydrogen Bonds in Peptide 310 Helices by3hJN,C′ Scalar Couplings

2004 ◽  
Vol 43 (24) ◽  
pp. 3152-3155 ◽  
Author(s):  
Massimo Bellanda ◽  
Mario Rainaldi ◽  
Quirinus B. Broxterman ◽  
Bernard Kaptein ◽  
Fernando Formaggio ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Direct Observation ◽  
Scalar Couplings ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

Intermolecular31P−15N and31P−1H Scalar Couplings Across Hydrogen Bonds Formed between a Protein and a Nucleotide

2000 ◽  
Vol 122 (24) ◽  
pp. 5883-5884 ◽  
Author(s):  
Masaki Mishima ◽  
Minoru Hatanaka ◽  
Shigeyuki Yokoyama ◽  
Takahisa Ikegami ◽  
Markus Wälchli ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Scalar Couplings

Insights into biomolecular hydrogen bonds from hydrogen bond scalar couplings

2004 ◽  
Vol 45 (3-4) ◽  
pp. 275-300 ◽  
Author(s):  
Stephan Grzesiek ◽  
Florence Cordier ◽  
Victor Jaravine ◽  
Michael Barfield
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Scalar Couplings

scholarly journals Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble

2021 ◽  
Author(s):  
Akinori Kidera ◽  
Kei Moritsugu ◽  
Toru Ekimoto ◽  
Mitsunori Ikeguchi
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Ligand Binding ◽  
Structural Information ◽  
Data Bank ◽  
Drug Candidate ◽  
Dynamic Regulation ◽  
Catalytic Function ◽  
Domain Iii ◽  
Structure Ensemble

The 3C-like protease (3CLpro) of SARS-CoV-2 is a potential therapeutic target for COVID-19. Importantly, it has an abundance of structural information solved as a complex with various drug candidate compounds. Collecting these crystal structures (83 Protein Data Bank (PDB) entries) together with those of the highly homologous 3CLpro of SARS-CoV (101 PDB entries), we constructed the crystal structure ensemble of 3CLpro to analyze the dynamic regulation of its catalytic function. The structural dynamics of the 3CLpro dimer observed in the ensemble were characterized by the motions of four separate loops (the C-loop, E-loop, H-loop, and Linker) and the C-terminal domain III on the rigid core of the chymotrypsin fold. Among the four moving loops, the C-loop (also known as the oxyanion binding loop) causes the order (active)-disorder (collapsed) transition, which is regulated cooperatively by five hydrogen bonds made with the surrounding residues. The C-loop, E-loop, and Linker constitute the major ligand binding sites, which consist of a limited variety of binding residues including the substrate binding subsites. Ligand binding causes a ligand size dependent conformational change to the E-loop and Linker, which further stabilize the C-loop via the hydrogen bond between the C-loop and E-loop. The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro.

scholarly journals Redetermination of the solvent-free crystal structure of L-proline

2018 ◽  
Vol 74 (8) ◽  
pp. 1067-1070 ◽  
Author(s):  
Jonas J. Koenig ◽  
Jörg-M. Neudörfl ◽  
Anne Hansen ◽  
Martin Breugst
Keyword(s):  
Crystal Structure ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Title Compound ◽  
Structural Information ◽  
Water Molecules ◽  
Two Dimensional ◽  
Zwitterionic Form ◽  
Dimensional Network

The title compound, (S)-pyrrolidine-2-carboxylic acid (C5H9NO2), commonly known as L-proline, crystallized without the inclusion of any solvent or water molecules through the slow diffusion of diethyl ether into a saturated solution of L-proline in ethanol. L-Proline crystallized in its zwitterionic form and the molecules are linked via N—H...O hydrogen bonds, resulting in a two-dimensional network. In comparison to the only other publication of a single-crystal structure of L-proline without inclusions [Kayushina & Vainshtein (1965). Kristallografiya, 10, 833–844], the R 1 value is significantly improved (0.039 versus 0.169) and thus, our data provides higher precision structural information.

Direct Observation of Intramolecular Hydrogen Bonds in Peptide 310 Helices by3hJN,C′ Scalar Couplings

2004 ◽  
Vol 116 (24) ◽  
pp. 3214-3217 ◽  
Author(s):  
Massimo Bellanda ◽  
Mario Rainaldi ◽  
Quirinus B. Broxterman ◽  
Bernard Kaptein ◽  
Fernando Formaggio ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Direct Observation ◽  
Scalar Couplings ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen
Sign in / Sign up

Export Citation Format

Share Document