Sequence Determinants of a Protein Folding Pathway

Nishimura, Chiaki; Lietzow, Michael A.; Dyson, H. Jane; Wright, Peter E.

doi:10.1016/j.jmb.2005.06.017

Cited by 51 publications

(71 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5 as a model of one of the earliest hydrophobic cores to be formed along the folding pathway (22,23); this model confirms the predicted folding interaction site (3) at residues 103-115. In the GW mutants (23), replacement of the tryptophan side chain from the A helix to the E helix preserves these contacts in the final folded form of the protein, but alters the sequence of formation of helices that are solvent-protected in the first steps of the folding pathway.…”

Section: Discussionsupporting

confidence: 70%

“…Application of the second approach (8), and conformational-energy calculations, led to the suggestion that interactions among the A, G, and H helices of apomyoglobin might be important for folding initiation (19), consistent with experimental results that implicated these regions in equilibrium intermediates of apomyoglobin (20) and in the earliest kinetic steps in the folding pathway (21). Recent experimental studies of mutants of myoglobin (22,23) provide convincing support for models that incorporate hydrophobic initiation and propagation of folding.…”

Section: Experimental Verification Of Modelssupporting

confidence: 63%

“…A key concept in our present understanding of the initiation process was the recognition (3, 6, 10) that large polar or charged amino acid side chains could be included in the groups of hydrophobic amino acids, and could thus contribute to the hydrophobic stabilization of the initial folded structures, through interactions of the nonpolar CH 2 groups between the backbone and the heteroatom functional groups. Experimental tests of this hypothesis (22,23) have shown definitively that, at least in the case of the helical protein apomyoglobin, the earliest events in the folding of the protein can be re-engineered precisely by making simple changes in the amino acid sequence based on the positions of key nonpolar groups.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

The role of hydrophobic interactions in initiation and propagation of protein folding

Dyson

Wright

Scheraga

2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

280

217

View full text Add to dashboard Cite

Globular proteins fold by minimizing the nonpolar surface that is exposed to water, while simultaneously providing hydrogenbonding interactions for buried backbone groups, usually in the form of secondary structures such as ␣-helices, ␤-sheets, and tight turns. A primary thermodynamic driving force for the formation of globular structure is thus the sequestration of nonpolar groups, but the correlation between the parts of proteins that are observed to fold first (termed folding initiation sites) and the ''hydrophobicity'' (as customarily defined) of the amino acids in these regions has been quite weak. It has previously been noted that many amino acid side chains contain considerable nonpolar sections, even if they also contain polar or charged groups. For example, a lysine side chain contains four methylenes, which may undergo hydrophobic interactions if the charged -NH 3 ؉ group is saltbridged or hydrogen-bonded. Folding initiation sites might therefore contain not only accepted ''hydrophobic'' amino acids, but also larger charged side chains. Recent experiments on the folding of mutant apomyoglobins provides corroboration for models based on the hypothesis that folding initiation sites arise from hydrophobic interactions. A near-perfect correlation was observed between the areas of the molecule that are present in the burstphase kinetic intermediate and both the free energy of formation of hydrophobic initiation sites and the parameter ''average area buried upon folding,'' which pinpoints large side chains, even those containing charged or polar portions. These results provide a putative mechanism for the control of protein-folding initiation and growth by polar͞nonpolar sequence propensity alone.folding pathways ͉ myoglobin ͉ ribonuclease F reed of the ribosome, and in the absence of chaperones, a newly synthesized protein exists in an ensemble of states, the so-called statistical coil, the nature of which is a subject of much recent investigation (1). It subsequently folds to the native biologically active structure whose free energy is considered to be a minimum under appropriate solution conditions (2). Since the seminal work of Anfinsen (2), the kinetics of the folding process and the final structure have been considered to be determined by the physical interactions among the amino acid residues to attain the thermodynamically favored state.A major question has involved the exact mechanism by which the interresidue interactions specify the initiation of folding in the unfolded polypeptide chain under folding conditions. Because nonpolar groups are not soluble in water, attention has been focused on the hydrophobic interactions between nonpolar side chains to achieve their sequestration from aqueous solvent. A model has been proposed in which nearby nonpolar groups in the chain participate in hydrophobic interactions with minimal loss of entropy of the chain because of the proximity of the interacting side chains in the amino acid sequence (3).Yet the chemical nature of the polypeptide chain complicates ...

show abstract

Section: Discussionsupporting

confidence: 70%

Section: Experimental Verification Of Modelssupporting

confidence: 63%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

The role of hydrophobic interactions in initiation and propagation of protein folding

Dyson

Wright

Scheraga

2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

280

217

View full text Add to dashboard Cite

show abstract

“…This quantity, a modified hydrophobicity parameter that takes into account the hydrophobic nature of many long "hydrophilic" side chains, 24 appears to be an excellent predictor of regions of apomyoglobin that are folded most rapidly. 25 This relationship also appears to hold for apoleghemoglobin: those regions of the amino acid sequence that correspond to peaks in the AABUF are also the locations of highest proton occupancy in the burst phase intermediate. Most of the residues in the G and H helix regions are protected in the burst phase intermediate; protection decreases towards the termini of the helical regions, consistent with end-fraying of the helices.…”

Section: High-resolution Structural Information On the Kinetic Intermmentioning

confidence: 84%

The Kinetic and Equilibrium Molten Globule Intermediates of Apoleghemoglobin Differ in Structure

Nishimura

Dyson

Wright

2008

Journal of Molecular Biology

Self Cite

View full text Add to dashboard Cite

An important question in protein folding is whether molten globule states formed under equilibrium conditions are good structural models for kinetic folding intermediates. The structures of the kinetic and equilibrium intermediates in the folding of the plant globin apoleghemoglobin have been compared at high resolution by quench-flow pH-pulse labeling and interrupted H/D exchange analyzed in DMSO solvent. Unlike its well-studied homolog, apomyoglobin, where the equilibrium and kinetic intermediates are quite similar, there are striking structural differences between the intermediates formed by apoleghemoglobin. In the kinetic intermediate, formed during the burst phase of the quench flow experiment, protected amides and helical structure are found mainly in the regions corresponding to the G and H helices of the folded protein, and in parts of the E helix and CE loop regions, whereas in the equilibrium intermediate, amide protection and helical structure are seen in parts of the A and B helix regions, as well as in the G and H regions, and the E helix remains largely unfolded. These results suggest that the structure of the molten globule intermediate of apoleghemoglobin is more plastic than that of apomyoglobin, so that it is readily transformed depending on the solution conditions, particularly pH. Thus, in the case of apoleghemoglobin at least, the equilibrium molten globule formed under destabilizing conditions at acid pH is not a good model for the compact intermediate formed during kinetic refolding experiments. Our high-precision kinetic analysis also reveals an additional slow phase during the folding of apoleghemoglobin, which is not observed for apomyoglobin. Hydrogen exchange pulse labeling experiments show that the slow folding phase is associated with residues in the C-E loop, which probably forms non-native structure in the intermediate that must be resolved before folding can proceed to completion.

show abstract

“…These experiments support the conclusion that specific NLIs between hydrophobic residue clusters can develop in a diffusion limited search at the initiation of the refolding transition. The correlation of fast structure formation with the average area buried upon folding that was determined for specific chain segments in the refolding apomyoglobin molecules further demonstrated the role of NLIs in the initiation of the folding transition (Nishimura et al 2005;Felitsky et al 2008). Lapidus et al (2007) used microsecond resolution of a microfluidic device for rapid mixing and resolved the initial phases of refolding of three model proteins.…”

Section: Direct and Indirect Findings Consistent With The Closed Longmentioning

confidence: 91%

The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways

et al. 2013

View full text Add to dashboard Cite

The extremely fast and efficient folding transition (in seconds) of globular proteins led to the search for some unifying principles embedded in the physics of the folding polypeptides. Most of the proposed mechanisms highlight the role of local interactions that stabilize secondary structure elements or a folding nucleus as the starting point of the folding pathways, i.e., a "bottom-up" mechanism. Nonlocal interactions were assumed either to stabilize the nucleus or lead to the later steps of coalescence of the secondary structure elements. An alternative mechanism was proposed, an "up-down" mechanism in which it was assumed that folding starts with the formation of very few non-local interactions which form closed long loops at the initiation of folding. The possible biological advantage of this mechanism, the "loop hypothesis", is that the hydrophobic collapse is associated with ordered compactization which reduces the chance for degradation and misfolding. In the present review the experiments, simulations and theoretical consideration that either directly or indirectly support this mechanism are summarized. It is argued that experiments monitoring the time-dependent development of the formation of specifically targeted early-formed sub-domain structural elements, either long loops or secondary structure elements, are necessary. This can be achieved by the timeresolved FRET-based "double kinetics" method in combination with mutational studies. Yet, attempts to improve the time resolution of the folding initiation should be extended down to the sub-microsecond time regime in order to design experiments that would resolve the classes of proteins which first fold by local or non-local interactions.

show abstract

Sequence Determinants of a Protein Folding Pathway

Cited by 51 publications

References 41 publications

The role of hydrophobic interactions in initiation and propagation of protein folding

The role of hydrophobic interactions in initiation and propagation of protein folding

The Kinetic and Equilibrium Molten Globule Intermediates of Apoleghemoglobin Differ in Structure

The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways

Contact Info

Product

Resources

About