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Protein folding absent selection.

Labean TH, Butt TR, Kauffman SA, Schultes EA - Genes (Basel) (2011)

Bottom Line: To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins.Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences.Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.

View Article: PubMed Central - PubMed

Affiliation: Sequenomics LLC, 1428 Chanterelle Lane, Hillsborough, NC 27278, USA. labean@sequenomics.com.

ABSTRACT
Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.

No MeSH data available.


FE unfolding curves for two fusions with increasing GuHCl. For Ub71L (a) and Ub71h (b). GuHCl concentrations: solid circles 0.0 M, open circles 0.2 M, solid squares 0.5 M, open squares 1 M, solid triangles 1.6 M, open triangles 2.6 M, solid diamonds 3.6 M, open diamonds 4.5 M. Spectra were also taken in 6 M GuHCl (not shown). (c) Fraction unfolded was calculated by dividing total observed red shift by the red shift at each denaturant concentration. Data are given for Ub71L attached to ubiquitin (solid circles) and cleaved from ubiquitin (open circles) and for Ub71h attached to ubiquitin (solid squares).
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f5-genes-02-00608: FE unfolding curves for two fusions with increasing GuHCl. For Ub71L (a) and Ub71h (b). GuHCl concentrations: solid circles 0.0 M, open circles 0.2 M, solid squares 0.5 M, open squares 1 M, solid triangles 1.6 M, open triangles 2.6 M, solid diamonds 3.6 M, open diamonds 4.5 M. Spectra were also taken in 6 M GuHCl (not shown). (c) Fraction unfolded was calculated by dividing total observed red shift by the red shift at each denaturant concentration. Data are given for Ub71L attached to ubiquitin (solid circles) and cleaved from ubiquitin (open circles) and for Ub71h attached to ubiquitin (solid squares).

Mentions: Having found evidence for helical structure and hydrophobic collapse, we next probed the cooperativity of the unfolding transitions in the random-sequence domains. The wavelength of maximum tryptophan fluorescence was monitored with increasing denaturant concentration to determine if loss of collapsed structure occurred gradually (non-cooperative) or rapidly (cooperative). Twelve fusions were denatured by incremental addition of GuHCl followed by equilibration and measurement of FE spectra. Two data sets and their unfolding profiles are shown (Figure 5). Three of the twelve fusions gave unfolding profiles similar to that for Ub71h (Figure 5b-c) in which the red shift of the FE peak occurred almost uniformly across the entire range of denaturant concentrations. This type of profile is indicative of non-cooperative unfolding. The majority of fusions (nine out of twelve) yielded unfolding profiles resembling that for Ub71L (Figure 5a-c) in which the red shift occurred non-uniformly. In these cases, a rapid increase in FE peak wavelength over a fairly small GuHCl concentration range indicated cooperative transitions. In all nine cases, the cooperative unfolding transitions occurred at GuHCl concentrations between 1 and 1.5 M which is within the low end of the range observed for unfolding of biological proteins [44]. This result does not distinguish between native and partially-folded structures, since cooperative unfolding has been observed previously in partially-folded designed proteins [43–45] and in molten globule states of natural proteins [46].


Protein folding absent selection.

Labean TH, Butt TR, Kauffman SA, Schultes EA - Genes (Basel) (2011)

FE unfolding curves for two fusions with increasing GuHCl. For Ub71L (a) and Ub71h (b). GuHCl concentrations: solid circles 0.0 M, open circles 0.2 M, solid squares 0.5 M, open squares 1 M, solid triangles 1.6 M, open triangles 2.6 M, solid diamonds 3.6 M, open diamonds 4.5 M. Spectra were also taken in 6 M GuHCl (not shown). (c) Fraction unfolded was calculated by dividing total observed red shift by the red shift at each denaturant concentration. Data are given for Ub71L attached to ubiquitin (solid circles) and cleaved from ubiquitin (open circles) and for Ub71h attached to ubiquitin (solid squares).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3927614&req=5

f5-genes-02-00608: FE unfolding curves for two fusions with increasing GuHCl. For Ub71L (a) and Ub71h (b). GuHCl concentrations: solid circles 0.0 M, open circles 0.2 M, solid squares 0.5 M, open squares 1 M, solid triangles 1.6 M, open triangles 2.6 M, solid diamonds 3.6 M, open diamonds 4.5 M. Spectra were also taken in 6 M GuHCl (not shown). (c) Fraction unfolded was calculated by dividing total observed red shift by the red shift at each denaturant concentration. Data are given for Ub71L attached to ubiquitin (solid circles) and cleaved from ubiquitin (open circles) and for Ub71h attached to ubiquitin (solid squares).
Mentions: Having found evidence for helical structure and hydrophobic collapse, we next probed the cooperativity of the unfolding transitions in the random-sequence domains. The wavelength of maximum tryptophan fluorescence was monitored with increasing denaturant concentration to determine if loss of collapsed structure occurred gradually (non-cooperative) or rapidly (cooperative). Twelve fusions were denatured by incremental addition of GuHCl followed by equilibration and measurement of FE spectra. Two data sets and their unfolding profiles are shown (Figure 5). Three of the twelve fusions gave unfolding profiles similar to that for Ub71h (Figure 5b-c) in which the red shift of the FE peak occurred almost uniformly across the entire range of denaturant concentrations. This type of profile is indicative of non-cooperative unfolding. The majority of fusions (nine out of twelve) yielded unfolding profiles resembling that for Ub71L (Figure 5a-c) in which the red shift occurred non-uniformly. In these cases, a rapid increase in FE peak wavelength over a fairly small GuHCl concentration range indicated cooperative transitions. In all nine cases, the cooperative unfolding transitions occurred at GuHCl concentrations between 1 and 1.5 M which is within the low end of the range observed for unfolding of biological proteins [44]. This result does not distinguish between native and partially-folded structures, since cooperative unfolding has been observed previously in partially-folded designed proteins [43–45] and in molten globule states of natural proteins [46].

Bottom Line: To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins.Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences.Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.

View Article: PubMed Central - PubMed

Affiliation: Sequenomics LLC, 1428 Chanterelle Lane, Hillsborough, NC 27278, USA. labean@sequenomics.com.

ABSTRACT
Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.

No MeSH data available.