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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.


Effect of temperature on CD spectra of ubiquitin and fusion pool. CD spectra of (a) ubiquitin and (b) LIB71 are shown at 25 °C (solid line) and 75 °C (broken line). Data were collected as described in the Experimental Section, except using 10 repeat scans from 195 to 225 nm, in 10 °C increments with 10 minute equilibration time.
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f3-genes-02-00608: Effect of temperature on CD spectra of ubiquitin and fusion pool. CD spectra of (a) ubiquitin and (b) LIB71 are shown at 25 °C (solid line) and 75 °C (broken line). Data were collected as described in the Experimental Section, except using 10 repeat scans from 195 to 225 nm, in 10 °C increments with 10 minute equilibration time.

Mentions: To further demonstrate absolute differences between the secondary structure content of control ubiquitin and a fusion pool sample, CD spectra were monitored during the heat-induced loss of secondary structure (Figure 3). Melting experiments demonstrated the reduction of helical content in LIB71 and stability of the ubiquitin spectrum during the change from 25 °C to 75 °C. Ubiquitin has been shown to denature at approximately 85 °C [39]. The decrease in ellipticity observed for LIB71 protein was essentially linear with increasing temperature, as might be expected for a complex mixture of proteins with distinct melting temperatures (data not shown). The loss of CD signal with increasing temperature clearly demonstrates, independent of possible artifacts from data normalization and deconvolution, the presence of heat-labile secondary structure in the random-sequence extensions.


Protein folding absent selection.

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

Effect of temperature on CD spectra of ubiquitin and fusion pool. CD spectra of (a) ubiquitin and (b) LIB71 are shown at 25 °C (solid line) and 75 °C (broken line). Data were collected as described in the Experimental Section, except using 10 repeat scans from 195 to 225 nm, in 10 °C increments with 10 minute equilibration time.
© Copyright Policy
Related In: Results  -  Collection

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

f3-genes-02-00608: Effect of temperature on CD spectra of ubiquitin and fusion pool. CD spectra of (a) ubiquitin and (b) LIB71 are shown at 25 °C (solid line) and 75 °C (broken line). Data were collected as described in the Experimental Section, except using 10 repeat scans from 195 to 225 nm, in 10 °C increments with 10 minute equilibration time.
Mentions: To further demonstrate absolute differences between the secondary structure content of control ubiquitin and a fusion pool sample, CD spectra were monitored during the heat-induced loss of secondary structure (Figure 3). Melting experiments demonstrated the reduction of helical content in LIB71 and stability of the ubiquitin spectrum during the change from 25 °C to 75 °C. Ubiquitin has been shown to denature at approximately 85 °C [39]. The decrease in ellipticity observed for LIB71 protein was essentially linear with increasing temperature, as might be expected for a complex mixture of proteins with distinct melting temperatures (data not shown). The loss of CD signal with increasing temperature clearly demonstrates, independent of possible artifacts from data normalization and deconvolution, the presence of heat-labile secondary structure in the random-sequence extensions.

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.