Privileged hydration sites in aromatic side chains: effect on conformational equilibrium

2017 ◽  
Vol 19 (42) ◽  
pp. 28684-28695 ◽  
Author(s):  
Belén Hernández ◽  
Fernando Pflüger ◽  
Manuel Dauchez ◽  
Mahmoud Ghomi
Keyword(s):  
Conformational Equilibrium ◽  
Theoretical Calculations ◽  
Side Chains ◽  
Aromatic Side Chains

The most energetically favourable hydration sites of aromatic (Phe, Tyr, Trp and His) side chains revealed by DFT-based theoretical calculations.

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.

scholarly journals Study of a Conformational Equilibrium of Lisinopril by HPLC, NMR, and DFT

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Sondes Bouabdallah ◽  
Med Thaieb Ben Dhia ◽  
Med Rida Driss
Keyword(s):  
Experimental Data ◽  
Thermodynamic Parameters ◽  
Conformational Equilibrium ◽  
Theoretical Calculations ◽  
Nmr Data ◽  
Major Species ◽  
B3lyp Calculations

The isomerization of lisinopril has been investigated using chromatographic, NMR spectroscopic, and theoretical calculations. The NMR data, particularly the NOEDIFF experiments, show that the major species that was eluted first is thetransform. The proportion was 77% and 23% for thetransandcis, respectively. The thermodynamic parameters (ΔH,ΔS, andΔG) were determined by varying the temperature in the NMR experiments. The interpretations of the experimental data were further supported by DFT/B3LYP calculations.

Biosynthetic13C Labeling of Aromatic Side Chains in Proteins for NMR Relaxation Measurements

2006 ◽  
Vol 128 (8) ◽  
pp. 2506-2507 ◽  
Author(s):  
Kaare Teilum ◽  
Ulrika Brath ◽  
Patrik Lundström ◽  
Mikael Akke
Keyword(s):  
Nmr Relaxation ◽  
Side Chains ◽  
Relaxation Measurements ◽  
Aromatic Side Chains

scholarly journals Protein Native-State Stabilization by Placing Aromatic Side Chains in N-Glycosylated Reverse Turns

Science ◽  
2011 ◽  
Vol 331 (6017) ◽  
pp. 571-575 ◽  
Author(s):  
E. K. Culyba ◽  
J. L. Price ◽  
S. R. Hanson ◽  
A. Dhar ◽  
C.-H. Wong ◽  
...  
Keyword(s):  
Side Chains ◽  
Native State ◽  
Aromatic Side Chains
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