Formation of the Native Structure of Proteins: Inferences from the Kinetics of Denaturation and Renaturation

2008 ◽  
pp. 125-146
Author(s):  
Charles Tanford
Keyword(s):  
Native Structure ◽  
Kinetics Of ◽  
Structure Of Proteins

Citrate chelation as a potential mechanism against aluminum toxicity in cells: the role of calmodulin

1985 ◽  
Vol 63 (11) ◽  
pp. 1167-1175 ◽  
Author(s):  
Charles G. Suhayda ◽  
Alfred Haug
Keyword(s):  
Circular Dichroism ◽  
Conceptual Understanding ◽  
Aluminum Toxicity ◽  
Hydrophobic Surface ◽  
Native Structure ◽  
Calcium Calmodulin Dependent ◽  
Α Helix ◽  
Kinetics Of ◽  
Circular Dichroïsm

At a molar excess of [citrate]/[aluminum], this organic acid can protect calmodulin from aluminum binding if the metal is presented to the protein in stoichiometric micromolar quantities, as judged by fluorescence and circular dichroism spectroscopy. Similar citrate concentrations are also capable of fully restoring calmodulin's hydrophobic surface exposure to that of the native protein when calmodulin was initially damaged by aluminum binding. Fluoride anions are equally effective in restoring calmodulin's native structure as determined by fluorescence spectroscopy. Measurements of the kinetics of citrate-mediated aluminum removal also indicated that the metal ions are completely removed from calmodulin, consistent with results derived from atomic absorption experiments. On the other hand, results from circular dichroism studies indicated that citrate-mediated aluminum removal from calmodulin can only partially restore the α-helix content to that originally present in apocalmodulin or in calcium–calmodulin, dependent upon the absence or presence of calcium ions. The results that chelators like citrate can protect calmodulin from aluminum injury may provide a conceptual understanding of physiological observations regarding aluminum-tolerant plant species which are generally rich in certain organic acids.

scholarly journals Codon 129 polymorphism of the human prion protein influences the kinetics of amyloid formation

2006 ◽  
Vol 87 (8) ◽  
pp. 2443-2449 ◽  
Author(s):  
Patrick A. Lewis ◽  
M. Howard Tattum ◽  
Samantha Jones ◽  
Daljit Bhelt ◽  
Mark Batchelor ◽  
...  
Keyword(s):  
Prion Protein ◽  
Amyloid Fibrils ◽  
Prion Diseases ◽  
Amyloid Formation ◽  
Native Structure ◽  
Prion Strain ◽  
Profound Influence ◽  
Human Prion Protein ◽  
Kinetics Of ◽  
Codon 129

The human prion protein (PrP) has a common polymorphism at residue 129, which can be valine or methionine. This polymorphism has a strong influence on susceptibility to prion diseases and on prion-strain properties. Previous work has shown that this amino acid variation has no measurable effect on the native structure of cellular PrP (PrPC). Here, it is shown that the polymorphism does not change the efficiency of conversion to the β-PrP conformation or affect the binding of copper(II) ions. However, in a partially denatured conformation, the polymorphic variation has a profound influence on the ability of the protein to form amyloid fibrils spontaneously.

What does protein refolding in vitro tell us about protein folding in the cell?

1993 ◽  
Vol 339 (1289) ◽  
pp. 287-295 ◽  
Keyword(s):  
Protein Folding ◽  
Molecular Chaperones ◽  
Side Reaction ◽  
Kinetic Mechanism ◽  
Structural Elements ◽  
Native Structure ◽  
Extrinsic Factors ◽  
Structure Of Proteins

The classical in vitro denaturation-renaturation studies by Anson, Anfinsen, Neurath, Pauling and others clearly suggested that the primary structure of proteins determines all higher levels of protein structure. Protein folding in the cell is inaccessible to a detailed analysis of its kinetic mechanism. There are obvious differences: nascent proteins acquire their native structure co- and post-translationally, with half-times in the minutes range, whereas refolding starts from the complete polypeptide chain, with rates varying from seconds to days. In the cell, accessory proteins are involved in regulating the rate of folding and association. Their role can be analysed both in vivo , by mutant studies, or by coexpression together with recombinant model proteins, and in vitro , by folding experiments in the absence and in the presence of 'foldases’ and molecular chaperones, with the following general results: (i) folding is a sequential process involving native-like structural elements and a ‘collapsed state’ as early intermediates; (ii) the major side-reaction is caused by ‘kinetic partitioning’ between correct folding and wrong aggregation; (iii) rate-determining steps may be assisted by protein disulphide isomerase, peptidyl prolyl- cys - trans -isomerase, and molecular chaperones; and (iv) extrinsic factors, not encoded in the amino acid sequence, may be of crucial importance.

scholarly journals Study of cryoprotectors effect on oxidation processes at storage of frozen halffinished products

2016 ◽  
Vol 10 (4) ◽  
Author(s):  
O. Glushkov
Keyword(s):  
Secondary Structure ◽  
Lipid Fraction ◽  
Technological Properties ◽  
Native Structure ◽  
Secondary Products ◽  
Oxidation Processes ◽  
Oxidative Processes ◽  
Kinetics Of

The publication presents data on the effect of polysaccharides as cryoprotectants on changes of the lipid fraction of quick-frozen semi-finished products during storage. Since the structure of minced systems is formed as a result of the destruction of the native structure of the meat and the formation of a new secondary structure, it is important to establish the effect of cryoprotectants on the key functional and technological properties of meat systems after freezing, and in the process of storage. Based on studies of the kinetics of the oxidation of fat and accumulation data on the accumulation of the primary and secondary products of oxidation inhibition of oxidative processes has been found.

Radiation Effects on the Native Structure of Proteins: Fragmentation without Dissociation

1998 ◽  
Vol 352 (2) ◽  
pp. 281-287 ◽  
Author(s):  
J.H. Miller ◽  
D.A. Fedoronko ◽  
B.D. Hass ◽  
M. Myint ◽  
E.S. Kempner
Keyword(s):  
Radiation Effects ◽  
Native Structure ◽  
Structure Of Proteins

scholarly journals Size and topology modulate the effects of frustration in protein folding

2018 ◽  
Vol 115 (37) ◽  
pp. 9234-9239 ◽  
Author(s):  
Alex Kluber ◽  
Timothy A. Burt ◽  
Cecilia Clementi
Keyword(s):  
Protein Folding ◽  
Folding Kinetics ◽  
Native Structure ◽  
And Topology ◽  
Folding Dynamics ◽  
Helical Proteins ◽  
Experimental Findings ◽  
State Size ◽  
Kinetics Of ◽  
Β Sheet

The presence of conflicting interactions, or frustration, determines how fast biomolecules can explore their configurational landscapes. Recent experiments have provided cases of systems with slow reconfiguration dynamics, perhaps arising from frustration. While it is well known that protein folding speed and mechanism are strongly affected by the protein native structure, it is still unknown how the response to frustration is modulated by the protein topology. We explore the effects of nonnative interactions in the reconfigurational and folding dynamics of proteins with different sizes and topologies. We find that structural correlations related to the folded state size and topology play an important role in determining the folding kinetics of proteins that otherwise have the same amount of nonnative interactions. In particular, we find that the reconfiguration dynamics of α-helical proteins are more susceptible to frustration than β-sheet proteins of the same size. Our results may explain recent experimental findings and suggest that attempts to measure the degree of frustration due to nonnative interactions might be more successful with α-helical proteins.

scholarly journals Non-affine displacements encode collective conformational fluctuations in proteins

2019 ◽  
Author(s):  
Dube Dheeraj Prakashchand ◽  
Navjeet Ahalawat ◽  
Satyabrata Bandyopadhyay ◽  
Surajit Sengupta ◽  
Jagannath Mondal
Keyword(s):  
Free Energy ◽  
Structural Changes ◽  
Energy Landscape ◽  
Conformational Transitions ◽  
Free Energy Landscape ◽  
Native Structure ◽  
Markov State Model ◽  
Markov State ◽  
Hierarchical Complexity ◽  
Kinetics Of

AbstractIdentifying subtle conformational fluctuations underlying the dynamics of bio macro-molecules is crucial for resolving their free energy landscape. We show that a collective variable, originally proposed for crystalline solids, is able to filter out essential macro-molecular motions more efficiently than other approaches. While homogenous or ‘affine’ deformations of the biopolymer are trivial, biopolymer conformations are complicated by the occurrence of in-homogenous or ‘non-affine’ displacements of atoms relative to their positions in the native structure. We show that these displacements encode functionally relevant conformations of macromolecule and, in combination with a formalism based upon time-structured independent component analysis, quantitatively resolve the free energy landscape of a number of macromolecules of hierarchical complexity. The kinetics of conformational transitions among the basins can now be mapped within the framework of a Markov state model. The non-affine modes, obtained by projecting out homogenous fluctuations from the local displacements, are found to be responsible for local structural changes required for transitioning between pairs of macro states.

Direct observations of radiation-enhanced transformations in glass

1983 ◽  
Vol 41 ◽  
pp. 354-355
Author(s):  
J. F. DeNatale ◽  
D. G. Howitt
Keyword(s):  
Glass Matrix ◽  
Diffusion Mechanism ◽  
Bubble Formation ◽  
Silicate Glasses ◽  
Phase Decomposition ◽  
Direct Observations ◽  
Thin Foils ◽  
Oxygen Bubble ◽  
Electron Energy Loss ◽  
Kinetics Of

The electron irradiation of silicate glasses containing metal cations produces various types of phase separation and decomposition which includes oxygen bubble formation at intermediate temperatures figure I. The kinetics of bubble formation are too rapid to be accounted for by oxygen diffusion but the behavior is consistent with a cation diffusion mechanism if the amount of oxygen in the bubble is not significantly different from that in the same volume of silicate glass. The formation of oxygen bubbles is often accompanied by precipitation of crystalline phases and/or amorphous phase decomposition in the regions between the bubbles and the detection of differences in oxygen concentration between the bubble and matrix by electron energy loss spectroscopy cannot be discerned (figure 2) even when the bubble occupies the majority of the foil depth.The oxygen bubbles are stable, even in the thin foils, months after irradiation and if van der Waals behavior of the interior gas is assumed an oxygen pressure of about 4000 atmospheres must be sustained for a 100 bubble if the surface tension with the glass matrix is to balance against it at intermediate temperatures.

Irradiation behavior of pyrolytic silicon carbide

1983 ◽  
Vol 41 ◽  
pp. 72-73
Author(s):  
R. J. Lauf
Keyword(s):  
Silicon Carbide ◽  
Fission Products ◽  
Thermodynamics And Kinetics ◽  
Neutron Fluences ◽  
Fuel Particles ◽  
Sic Coatings ◽  
Irradiation Behavior ◽  
Kinetics Of ◽  
Htgr Fuel

Fuel particles for the High-Temperature Gas-Cooled Reactor (HTGR) contain a layer of pyrolytic silicon carbide to act as a miniature pressure vessel and primary fission product barrier. Optimization of the SiC with respect to fuel performance involves four areas of study: (a) characterization of as-deposited SiC coatings; (b) thermodynamics and kinetics of chemical reactions between SiC and fission products; (c) irradiation behavior of SiC in the absence of fission products; and (d) combined effects of irradiation and fission products. This paper reports the behavior of SiC deposited on inert microspheres and irradiated to fast neutron fluences typical of HTGR fuel at end-of-life.

The Ordered Phase Formation in Ti-Al-Ga Alloys

1970 ◽  
Vol 28 ◽  
pp. 440-441
Author(s):  
Shiro Fujishiro ◽  
Harold L. Gegel
Keyword(s):  
Thermal Stability ◽  
High Temperature ◽  
Titanium Alloys ◽  
Growth Kinetics ◽  
Stoichiometric Composition ◽  
Good Potential ◽  
Alpha Titanium ◽  
Cold Rolled ◽  
Kinetics Of ◽  
Thermal Stability Of

Ordered-alpha titanium alloys having a DO19 type structure have good potential for high temperature (600°C) applications, due to the thermal stability of the ordered phase and the inherent resistance to recrystallization of these alloys. Five different Ti-Al-Ga alloys consisting of equal atomic percents of aluminum and gallium solute additions up to the stoichiometric composition, Ti3(Al, Ga), were used to study the growth kinetics of the ordered phase and the nature of its interface.The alloys were homogenized in the beta region in a vacuum of about 5×10-7 torr, furnace cooled; reheated in air to 50°C below the alpha transus for hot working. The alloys were subsequently acid cleaned, annealed in vacuo, and cold rolled to about. 050 inch prior to additional homogenization

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