Structural determinants of protein folding

Kang, Taewook; Kini, R. Manjunatha

doi:10.1007/s00018-009-0023-5

Cited by 23 publications

(12 citation statements)

References 242 publications

(261 reference statements)

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“… 17 Several aspects influencing the folding, such as the number of hydroxyproline residues, the loop size between the two linked cysteines, or amidation of the C-terminus, are discussed controversially in the literature without a clear preference indicating the uniqueness of each sequence and the respective biological activity. 17 , 28 , 33 , 34 …”

Section: Resultsmentioning

confidence: 99%

Insights into the Folding of Disulfide-Rich μ-Conotoxins

et al. 2018

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The study of protein conformations using molecular dynamics (MD) simulations has been in place for decades. A major contribution to the structural stability and native conformation of a protein is made by the primary sequence and disulfide bonds formed during the folding process. Here, we investigated μ-conotoxins GIIIA, KIIIA, PIIIA, SIIIA, and SmIIIA as model peptides possessing three disulfide bonds. Their NMR structures were used for MD simulations in a novel approach studying the conformations between the folded and the unfolded states by systematically breaking the distinct disulfide bonds and monitoring the conformational stability of the peptides. As an outcome, the use of a combination of the existing knowledge and results from the simulations to classify the studied peptides within the extreme models of disulfide folding pathways, namely the bovine pancreatic trypsin inhibitor pathway and the hirudin pathway, is demonstrated. Recommendations for the design and synthesis of cysteine-rich peptides with a reduced number of disulfide bonds conclude the study.

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Section: Resultsmentioning

confidence: 99%

Insights into the Folding of Disulfide-Rich μ-Conotoxins

et al. 2018

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“…The structural properties of this ensemble in terms of its coiling propensities crucially determine its transition to the native fold, or, the transition to and function of the collapsed state of an intrinsically disordered protein. [1][2][3][4] The characterization of the unfolded state by experiments and simulations, however, is a major obstacle due to its structural heterogeneity. Recently, single molecule approaches, namely fluorescence resonance energy transfer and force spectroscopy, have allowed the examination of the random coil properties and collapse tendencies of protein unfolded states by measuring end-to-end distances as a function of chemical denaturants and force, respectively.…”

Section: Introductionmentioning

confidence: 99%

Glycosylation Enhances Peptide Hydrophobic Collapse by Impairing Solvation

et al. 2010

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Post-translational N-glycosylation of proteins is ubiquitous in eukaryotic cells, and has been shown to influence the thermodynamics of protein collapse and folding. However, the mechanism for this influence is not well understood. All-atom molecular dynamics simulations are carried out to study the collapse of a peptide linked to a single N-glycan. The glycan is shown to perturb the local water hydrogen-bonding network, rendering it less able to solvate the peptide and thus enhancing the hydrophobic contribution to the free energy of collapse. The enhancement of the hydrophobic collapse compensates for the weakened entropic coiling due to the bulky glycan chain and leads to a stronger burial of hydrophobic surface, presumably enhancing folding. This conclusion is reinforced by comparison with coarse-grained simulations, which contain no explicit solvent and correspondingly exhibit no significant thermodynamic changes on glycosylation.

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“…Alternative splicing produces different proteins from the same DNA sequence which, again, reinforces the fact that the DNA-protein relationship is not univocal. Moreover, against what was postulated by Anfinsen (Anfinsen, 1973), protein folding is not entirely determined from its amino acid sequence either 6 (Kang and Kini 2009a). …”

Section: Introductionmentioning

confidence: 81%

“… 6 “In essence, the determinants of correct folding (or in the case of amyloidogenesis, protein misfolding) are neither completely understood nor can they be simplistically limited to structural features on the sequence” (Kang and Kini 2009b). …”

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confidence: 99%

Is information a proper observable for biological organization?

Longo

Miquel²,

Sonnenschein

et al. 2012

Progress in Biophysics and Molecular Biology

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In the last century, jointly with the advent of computers, mathematical theories of information were developed. Shortly thereafter, during the ascent of molecular biology, the concept of information was rapidly transferred into biology at large. Several philosophers and biologists have argued against adopting this concept based on epistemological and ontological arguments, and also, because it encouraged genetic determinism. While the theories of elaboration and transmission of information are valid mathematical theories, their own logic and implicit causal structure make them inimical to biology, and because of it, their applications have and are hindering the development of a sound theory of organisms. Our analysis concentrates on the development of information theories in mathematics and on the differences between these theories regarding the relationship among complexity, information and entropy.

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Structural determinants of protein folding

Cited by 23 publications

References 242 publications

Insights into the Folding of Disulfide-Rich μ-Conotoxins

Insights into the Folding of Disulfide-Rich μ-Conotoxins

Glycosylation Enhances Peptide Hydrophobic Collapse by Impairing Solvation

Is information a proper observable for biological organization?

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