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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.


Related in: MedlinePlus

Fluorescence emission (FE) spectra of fusion protein pools (a) LIB38; and (b) LIB71. The spectra were taken in water (solid lines) and in 6 M GuHCl (broken lines). Decreased intensity and red shift of the emission wavelength maximum in GuHCl indicate protein unfolding and tryptophan exposure. The fluorescence emission of ubiquitin in this range was low and unaffected by GuHCl.
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f4-genes-02-00608: Fluorescence emission (FE) spectra of fusion protein pools (a) LIB38; and (b) LIB71. The spectra were taken in water (solid lines) and in 6 M GuHCl (broken lines). Decreased intensity and red shift of the emission wavelength maximum in GuHCl indicate protein unfolding and tryptophan exposure. The fluorescence emission of ubiquitin in this range was low and unaffected by GuHCl.

Mentions: The two protein pools as well as 25 tryptophan-containing individual fusions were examined using FE spectroscopy under native and denaturing conditions. The spectra for LIB38 and LIB71 both show a red shift and decrease in intensity in the presence of 6 M GuHCl, consistent with protection of tryptophan from water in the absence of denaturant and exposure in its presence (Figure 4). This observation provides evidence of collapsed states in a large population of proteins in each fusion library. The change in emission intensity is also an indicator of structural alterations near tryptophan residues; however the direction and magnitude of such changes are unpredictable [41]. The reason for a larger red-shift and smaller intensity change in the LIB71 spectra versus that for LIB38 remains unclear. A large majority (19 out of 25) of the individual fusions examined also showed tryptophan protection. To test refolding of the random-sequence, reprotection of tryptophan was examined after performing buffer exchange from 6 M GuHCl back into Tris buffer. Reprotection was demonstrated for all six fusions tested (data not shown), thus collapsed structure is a property of the novel extensions, independent of in vivo protein biosynthesis.


Protein folding absent selection.

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

Fluorescence emission (FE) spectra of fusion protein pools (a) LIB38; and (b) LIB71. The spectra were taken in water (solid lines) and in 6 M GuHCl (broken lines). Decreased intensity and red shift of the emission wavelength maximum in GuHCl indicate protein unfolding and tryptophan exposure. The fluorescence emission of ubiquitin in this range was low and unaffected by GuHCl.
© Copyright Policy
Related In: Results  -  Collection

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

f4-genes-02-00608: Fluorescence emission (FE) spectra of fusion protein pools (a) LIB38; and (b) LIB71. The spectra were taken in water (solid lines) and in 6 M GuHCl (broken lines). Decreased intensity and red shift of the emission wavelength maximum in GuHCl indicate protein unfolding and tryptophan exposure. The fluorescence emission of ubiquitin in this range was low and unaffected by GuHCl.
Mentions: The two protein pools as well as 25 tryptophan-containing individual fusions were examined using FE spectroscopy under native and denaturing conditions. The spectra for LIB38 and LIB71 both show a red shift and decrease in intensity in the presence of 6 M GuHCl, consistent with protection of tryptophan from water in the absence of denaturant and exposure in its presence (Figure 4). This observation provides evidence of collapsed states in a large population of proteins in each fusion library. The change in emission intensity is also an indicator of structural alterations near tryptophan residues; however the direction and magnitude of such changes are unpredictable [41]. The reason for a larger red-shift and smaller intensity change in the LIB71 spectra versus that for LIB38 remains unclear. A large majority (19 out of 25) of the individual fusions examined also showed tryptophan protection. To test refolding of the random-sequence, reprotection of tryptophan was examined after performing buffer exchange from 6 M GuHCl back into Tris buffer. Reprotection was demonstrated for all six fusions tested (data not shown), thus collapsed structure is a property of the novel extensions, independent of in vivo protein biosynthesis.

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.


Related in: MedlinePlus