scholarly journals Ring Flips Revisited: 13C Relaxation Dispersion Measurements of Aromatic Side Chain Dynamics and Activation Barriers in Basic Pancreatic Trypsin Inhibitor

Biochemistry ◽  
2014 ◽  
Vol 53 (28) ◽  
pp. 4519-4525 ◽  
Author(s):  
Ulrich Weininger ◽  
Kristofer Modig ◽  
Mikael Akke
Keyword(s):  
Trypsin Inhibitor ◽  
Relaxation Dispersion ◽  
Side Chain ◽  
Aromatic Side Chain ◽  
Chain Dynamics ◽  
Activation Barriers ◽  
Basic Pancreatic Trypsin Inhibitor ◽  
Pancreatic Trypsin Inhibitor ◽  
13C Relaxation ◽  
Side Chain Dynamics

scholarly journals Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics

2021 ◽  
Author(s):  
Pär Söderhjelm ◽  
Mandar Kulkarni
Keyword(s):  
Free Energy ◽  
Trypsin Inhibitor ◽  
Side Chain ◽  
Side Chains ◽  
Aromatic Residues ◽  
Basic Pancreatic Trypsin Inhibitor ◽  
Pancreatic Trypsin Inhibitor ◽  
Energy Surfaces ◽  
Aromatic Side Chains

Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180° around the Cβ-Cγ axis (χ2 dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate that χ2 as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues needed χ1 (N−Cχα) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.

Histidine side-chain dynamics and protonation monitored by 13C CPMG NMR relaxation dispersion

2009 ◽  
Vol 44 (4) ◽  
pp. 225-233 ◽  
Author(s):  
Mathias A. S. Hass ◽  
Ali Yilmaz ◽  
Hans E. M. Christensen ◽  
Jens J. Led
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Side Chain ◽  
Chain Dynamics ◽  
Side Chain Dynamics

Binding of the bovine basic pancreatic trypsin inhibitor (Kunitz) to human Lys77-plasmin

1986 ◽  
Vol 191 (2) ◽  
pp. 295-297 ◽  
Author(s):  
Enea Menegatti ◽  
Mario Guarneri ◽  
Martino Bolognesi ◽  
Paolo Ascenzi ◽  
Gino Amiconi
Keyword(s):  
Trypsin Inhibitor ◽  
Basic Pancreatic Trypsin Inhibitor ◽  
Pancreatic Trypsin Inhibitor

scholarly journals Hydrophobic Core Mutations in CI2 Globally Perturb Fast Side-Chain Dynamics Similarly without Regard to Position†

Biochemistry ◽  
2008 ◽  
Vol 47 (33) ◽  
pp. 8566-8576 ◽  
Author(s):  
Matthew J. Whitley ◽  
Jun Zhang ◽  
Andrew L. Lee
Keyword(s):  
Side Chain ◽  
Hydrophobic Core ◽  
Chain Dynamics ◽  
Side Chain Dynamics

Arginine side-chain dynamics in the HIV-1 Rev-RRE complex 1 1Edited by M. F. Summers

2000 ◽  
Vol 303 (4) ◽  
pp. 515-529 ◽  
Author(s):  
Thomas A. Wilkinson ◽  
Maria Victoria Botuyan ◽  
Bruce E. Kaplan ◽  
John J. Rossi ◽  
Yuan Chen
Keyword(s):  
Side Chain ◽  
Chain Dynamics ◽  
Arginine Side Chain ◽  
Side Chain Dynamics ◽  
Hiv 1

Monitoring Side-Chain Dynamics of Proteins Using 2H Relaxation

2013 ◽  
pp. 3-27 ◽  
Author(s):  
Chad M. Petit ◽  
Andrew L. Lee
Keyword(s):  
Side Chain ◽  
Chain Dynamics ◽  
Side Chain Dynamics

scholarly journals Backbone and side-chain dynamics of residues in a partially folded β-sheet peptide from platelet factor-4

1997 ◽  
Vol 6 (2) ◽  
pp. 355-363 ◽  
Author(s):  
Vladimir A. Daragan ◽  
Elena E. Ilyina ◽  
Cynthia G. Fields ◽  
Gregg B. Fields ◽  
Kevin H. Mayo
Keyword(s):  
Platelet Factor 4 ◽  
Side Chain ◽  
Platelet Factor ◽  
Chain Dynamics ◽  
Β Sheet ◽  
Side Chain Dynamics
Sign in / Sign up

Export Citation Format

Share Document