PROTEIN FOLDING STAGES AND UNIVERSAL EXPONENTS

2010 ◽  
Vol 24 (20) ◽  
pp. 2113-2115 ◽  
Author(s):  
KERSON HUANG
Keyword(s):  
Protein Folding ◽  
Hydrogen Bonding ◽  
Computer Simulations ◽  
Power Law ◽  
Molten Globule ◽  
Hydrophobic Effect ◽  
Radius Of Gyration ◽  
Three Stages ◽  
Self Avoiding Walk

We propose three stages in protein folding, based on physical arguements involving the interplay between the hydrophobic effect and hydrogen bonding, and computer simulations using the CSAW (conditioned self-avoiding walk) model. These stages are characterized by universal exponents ν = 3/5, 3/7, 2/5 in the power law R ~ Nν, where R is the radius of gyration and N is the number of residues. They correspond to the experimentally observed stages: unfolded, preglobule, molten globule.

Models of cooperativity in protein folding

1995 ◽  
Vol 348 (1323) ◽  
pp. 61-70 ◽  
Keyword(s):  
Protein Folding ◽  
Molten Globule ◽  
Core Collapse ◽  
Hydrophobic Core ◽  
Model Studies ◽  
Helix Formation ◽  
Collapse Model ◽  
Folding Pathways ◽  
State Behaviour ◽  
Denatured States

What is the basis for the two-state cooperativity of protein folding? Since the 1950s, three main models have been put forward. 1. In ‘helix-coil’ theory, cooperativity is due to local interactions among near neighbours in the sequence. Helix-coil cooperativity is probably not the principal basis for the folding of globular proteins because it is not two-state, the forces are weak, it does not account for sheet proteins, and there is no evidence that helix formation precedes the formation of a hydrophobic core in the folding pathways. 2. In the ‘sidechain packing’ model, cooperativity is attributed to the jigsaw-puzzle-like complementary fits of sidechains. This too is probably not the basis of folding cooperativity because exact models and experiments on homopolymers with sidechains give no evidence that sidechain freezing is two-state, sidechain complementarities in proteins are only weak trends, and the molten globule model predicted by this model is far more native-like than experiments indicate. 3. In the ‘hydrophobic core collapse’ model, cooperativity is due to the assembly of non-polar residues into a good core. Exact model studies show that this model gives two-state behaviour for some sequences of hydrophobic and polar monomers. It is based on strong forces. There is considerable experimental evidence for the kinetics this model predicts: the development of hydrophobic clusters and cores is concurrent with secondary structure formation. It predicts compact denatured states with sizes and degrees of disorder that are in reasonable agreement with experiments.

Molecular Recognition and Photoprotection of Riboflavin in Water by a Biomimetic Host

2021 ◽  
Author(s):  
Hong Zhang ◽  
Li-Li Wang ◽  
Xin-Yu Pang ◽  
Liu-Pan Yang ◽  
Wei Jiang
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Recognition ◽  
Hydrophobic Effect ◽  
Water Soluble ◽  
Side Walls

A water-soluble tetralactam macrocycle with 2,6-diethoxynaphthalene group as side walls is able to strongly bind riboflavin (Ka >107 M−1) in water through hydrogen bonding and the hydrophobic effect. The encapsulated...

Three stages of hydrogen bonding network in DMF-water binary solution

2021 ◽  
Vol 324 ◽  
pp. 114996
Author(s):  
Bo Yang ◽  
Hongzhi Lang ◽  
Zhe Liu ◽  
Shenghan Wang ◽  
Zhiwei Men ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Binary Solution ◽  
Three Stages ◽  
Hydrogen Bonding Network

scholarly journals Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation

2011 ◽  
Vol 7 (10) ◽  
pp. e1002169 ◽  
Author(s):  
Anthony W. Fitzpatrick ◽  
Tuomas P. J. Knowles ◽  
Christopher A. Waudby ◽  
Michele Vendruscolo ◽  
Christopher M. Dobson
Keyword(s):  
Protein Folding ◽  
Hydrogen Bonding ◽  
Hydrogen Bonding Interactions

Biased continuous-time random walks for ordinary and equilibrium cases: facilitation of diffusion, ergodicity breaking and ageing

2018 ◽  
Vol 20 (32) ◽  
pp. 20827-20848 ◽  
Author(s):  
Ru Hou ◽  
Andrey G. Cherstvy ◽  
Ralf Metzler ◽  
Takuma Akimoto
Keyword(s):  
Random Walks ◽  
Computer Simulations ◽  
Power Law ◽  
Waiting Time ◽  
Continuous Time ◽  
Zero Drift ◽  
Renewal Processes ◽  
Waiting Time Distributions ◽  
Continuous Time Random Walks ◽  
Ergodicity Breaking

We examine renewal processes with power-law waiting time distributions and non-zero drift via computing analytically and by computer simulations their ensemble and time averaged spreading characteristics.

scholarly journals Molecular Interactions of Renin with Chikusetsusaponin IV and Momordin IIc

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Hai-Ling Zhang ◽  
Gui-Lan Zhu ◽  
Xiao-Tian Chen
Keyword(s):  
Hydrogen Bonding ◽  
Binding Sites ◽  
Driving Forces ◽  
Hydrophobic Interactions ◽  
Hydrophobic Effect ◽  
Energy Calculation ◽  
Total Binding Energy ◽  
Interaction Energies ◽  
Amino Acid Residues ◽  
Poisson Boltzmann

The paper dealt with the molecular mechanism for the binding sites and driving forces of renin with chikusetsusaponin IV and momordin IIc by means of molecular docking and free energy calculation based on the crystal structure. The result showed that renin and the saponins fit well. As shown by LigPlot + software analyzing the hydrogen bonding and hydrophobic effect between renin and the saponins, the amino acid residues such as Ser230, Tyr85, and Tyr201 form the hydrogen bonds, with S3sp, S3, and S2′ being the active pockets. In addition, there are relatively strong hydrophobic interactions of renin with saponins in S3sp, S3, S2, S1, S1′, and S2′, with Gly228, Val36, Ala229, Gln19, Met303, Gln135, Ser41, Ile137, Asp38, Arg82, and Tyr83 being the key amino acids. The dynamics reached equilibration after about 1000 ps simulation with average root-mean-square deviations of 0.222 nm and 0.217 nm. The molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) yielded −1.10812 kcal/mol and −39.0587 kcal/mol total binding energy for the two complexes, respectively, which were primarily contributed by electrostatic and van der Waals interaction energies, and the binding was strongly unfavored by polar solvation energy, a further confirmation that momordin IIc has stronger hydrogen bonding and hydrophobic effect in the inhibition of renin than the chikusetsusaponin IV.

Molten globule intermediates and protein folding

1991 ◽  
Vol 19 (5) ◽  
Author(s):  
H. Christensen ◽  
R.H. Pain
Keyword(s):  
Protein Folding ◽  
Molten Globule
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