Cotranslational Protein Folding and Terminus Hydrophobicity

Srivastava, Sheenal; Patton, Yumi; Fisher, David; Wood, Graham R.

doi:10.1155/2011/176813

Cited by 5 publications

(3 citation statements)

References 26 publications

(31 reference statements)

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“…Moreover, the positioning of hydrophobic clusters in the sequence may affect the folding pathway and dynamics e.g. [ 2 , 3 ]. Note that these stabilizing forces are partially compensated by the decrease in chain entropy upon folding.…”

Section: Introductionmentioning

confidence: 99%

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures

Dijk¹,

Hoogeveen²,

Abeln³

2015

PLoS Comput Biol

123

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The hydrophobic effect is the main driving force in protein folding. One can estimate the relative strength of this hydrophobic effect for each amino acid by mining a large set of experimentally determined protein structures. However, the hydrophobic force is known to be strongly temperature dependent. This temperature dependence is thought to explain the denaturation of proteins at low temperatures. Here we investigate if it is possible to extract this temperature dependence directly from a large set of protein structures determined at different temperatures. Using NMR structures filtered for sequence identity, we were able to extract hydrophobicity propensities for all amino acids at five different temperature ranges (spanning 265-340 K). These propensities show that the hydrophobicity becomes weaker at lower temperatures, in line with current theory. Alternatively, one can conclude that the temperature dependence of the hydrophobic effect has a measurable influence on protein structures. Moreover, this work provides a method for probing the individual temperature dependence of the different amino acid types, which is difficult to obtain by direct experiment.

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Section: Introductionmentioning

confidence: 99%

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures

Dijk¹,

Hoogeveen²,

Abeln³

2015

PLoS Comput Biol

123

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“…Among others, at least in some cases, cotranslational folding requires complete protein structural subdomains [107] , [108] . Cotranslational protein folding following the sense of translation (from the N terminal) predicts more accurately protein structures than when proceeding in the opposite sense (from the C terminal) [109] , [110] , indicating that cotranslational protein folding is a reality for most proteins. Nevertheless, cell free protein folding shows that cotranslational folding is not always required [111] .…”

Section: Translation Kineticsmentioning

confidence: 99%

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes

Seligmann

Warthi

2017

Computational and Structural Biotechnology Journal

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A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5′/3′ asymmetric (CDA = − 1/1; CDA = − 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (−/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2′/3′ hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5′-ZXX-3′/5′-XXZ-3′).

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“…The cotranslational folding process is controlled by translation speed and special ribosomal structure 2 13 14 15 16 . Experimental and theoretical studies on the cotranslational folding were highlighted and novel phenomena were observed 7 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 . For examples, it was found that the synthesized peptides take on definite secondary structures while they are growing on the ribosome 2 16 .…”

mentioning

confidence: 99%

Computational evidence that fast translation speed can increase the probability of cotranslational protein folding

Wang

Chen

et al. 2015

Sci Rep

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Translation speed can affect the cotranslational folding of nascent peptide. Experimental observations have indicated that slowing down translation rates of codons can increase the probability of protein cotranslational folding. Recently, a kinetic modeling indicates that fast translation can also increase the probability of cotranslational protein folding by avoiding misfolded intermediates. We show that the villin headpiece subdomain HP35 is an ideal model to demonstrate this phenomenon. We studied cotranslational folding of HP35 with different fast translation speeds by all-atom molecular dynamics simulations and found that HP35 can fold along a well-defined pathway that passes the on-pathway intermediate but avoids the misfolded off-pathway intermediate in certain case. This greatly increases the probability of HP35 cotranslational folding and the approximate mean first passage time of folding into native state is about 1.67μs. Since we also considered the space-confined effect of the ribosomal exit tunnel on the cotranslational folding, our simulation results suggested alternative mechanism for the increasing of cotranslational folding probability by fast translation speed.

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Cotranslational Protein Folding and Terminus Hydrophobicity

Cited by 5 publications

References 26 publications

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes

Computational evidence that fast translation speed can increase the probability of cotranslational protein folding

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