scholarly journals Time-dependent communication between multiple amino acids during protein folding

2021 ◽  
Vol 12 (16) ◽  
pp. 5944-5951
Author(s):  
Song-Ho Chong ◽  
Sihyun Ham
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Transition State ◽  
Time Dependent ◽  
Transition Path ◽  
Contact Formation ◽  
Molecular Origin

Cooperativity in contact formation among multiple amino acids starts to develop upon entering the folding transition path and attains a maximum at the folding transition state, providing the molecular origin of the two-state folding behavior.

scholarly journals Transition Path Times in Protein Folding Studied by Structure-Based Simulation

2015 ◽  
Vol 108 (2) ◽  
pp. 50a
Author(s):  
Mashiho Ito ◽  
Shoji Takada
Keyword(s):  
Protein Folding ◽  
Transition Path

scholarly journals Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape

2018 ◽  
Vol 122 (49) ◽  
pp. 11126-11136 ◽  
Author(s):  
William M. Jacobs ◽  
Eugene I. Shakhnovich
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Transition Path

scholarly journals Inverse enzyme isotope effects in human purine nucleoside phosphorylase with heavy asparagine labels

2018 ◽  
Vol 115 (27) ◽  
pp. E6209-E6216 ◽  
Author(s):  
Rajesh K. Harijan ◽  
Ioanna Zoi ◽  
Dimitri Antoniou ◽  
Steven D. Schwartz ◽  
Vern L. Schramm
Keyword(s):  
Transition State ◽  
Purine Nucleoside Phosphorylase ◽  
Isotope Effects ◽  
Catalytic Site ◽  
Path Sampling ◽  
Transition Path ◽  
Transition Path Sampling ◽  
Steady State Kinetics ◽  
Leaving Group ◽  
Transition State Barrier

Transition path-sampling calculations with several enzymes have indicated that local catalytic site femtosecond motions are linked to transition state barrier crossing. Experimentally, femtosecond motions can be perturbed by labeling the protein with amino acids containing 13C, 15N, and nonexchangeable 2H. A slowed chemical step at the catalytic site with variable effects on steady-state kinetics is usually observed for heavy enzymes. Heavy human purine nucleoside phosphorylase (PNP) is slowed significantly (kchemlight/kchemheavy = 1.36). An asparagine (Asn243) at the catalytic site is involved in purine leaving-group activation in the PNP catalytic mechanism. In a PNP produced with isotopically heavy asparagines, the chemical step is faster (kchemlight/kchemheavy = 0.78). When all amino acids in PNP are heavy except for the asparagines, the chemical step is also faster (kchemlight/kchemheavy = 0.71). Substrate-trapping experiments provided independent confirmation of improved catalysis in these constructs. Transition path-sampling analysis of these partially labeled PNPs indicate altered femtosecond catalytic site motions with improved Asn243 interactions to the purine leaving group. Altered transition state barrier recrossing has been proposed as an explanation for heavy-PNP isotope effects but is incompatible with these isotope effects. Rate-limiting product release governs steady-state kinetics in this enzyme, and kinetic constants were unaffected in the labeled PNPs. The study suggests that mass-constrained femtosecond motions at the catalytic site of PNP can improve transition state barrier crossing by more frequent sampling of essential catalytic site contacts.

3. Proteins

2021 ◽  
pp. 34-51
Author(s):  
Mark Lorch
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structure ◽  
Protein Structures ◽  
Structure And Function ◽  
Vast Array ◽  
A Cell ◽  
Cellular Machinery ◽  
And Function ◽  
The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

scholarly journals Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates

2006 ◽  
Vol 91 (1) ◽  
pp. 14-24 ◽  
Author(s):  
Christopher D. Snow ◽  
Young Min Rhee ◽  
Vijay S. Pande
Keyword(s):  
Protein Folding ◽  
Transition State ◽  
Reaction Coordinates ◽  
Definition Of

Identifying Importance of Amino Acids for Protein Folding from Crystal Structures

2003 ◽  
pp. 616-638 ◽  
Author(s):  
Nikolay V. Dokholyan ◽  
Jose M. Borreguero ◽  
Sergey V. Buldyrev ◽  
Feng Ding ◽  
H.Eugene Stanley ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Crystal Structures
Sign in / Sign up

Export Citation Format

Share Document