Native structural propensity in cellular retinoic acid-binding protein I 64–88: the role of locally encoded structure in the folding of a β-barrel protein

Rotondi, Kenneth S.; Rotondi, Linda F.; Gierasch, Lila M.

doi:10.1016/s0301-4622(02)00296-x

Cited by 12 publications

(22 citation statements)

References 56 publications

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“…Additionally, turns III and IV bridge the transition from the front to the back sheet. We found that these turns are also populated in a larger fragment encompassing both turns, 27 suggesting that they may influence the behavior of the polypeptide chain more globally. Due to the topological significance of the turn III-strand5-turn IV region, the local nature of the forces biasing the native conformation, and their persistence in a larger fragment, we hypothesized that this region of CRABP I behaves as a site of folding initiation.…”

Section: Introductionmentioning

confidence: 79%

“…Due to the topological significance of the turn III-strand5-turn IV region, the local nature of the forces biasing the native conformation, and their persistence in a larger fragment, we hypothesized that this region of CRABP I behaves as a site of folding initiation. 27 We wish to understand in greater depth the forces responsible for the native conformational bias exhibited by fragments corresponding to turns III and IV of CRABP I. The tendency of the peptide fragments to populate these turns must result from a combination of stabilizing hydrophobic and polar interactions in combination with steric restrictions at the residue level that favor turn formation.…”

Section: Introductionmentioning

confidence: 99%

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Local sequence information in cellular retinoic acid‐binding protein I: Specific residue roles in β‐turns*

Rotondi

Gierasch

2003

Biopolymers

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We have recently shown that two of the beta-turns (III and IV) in the ten-stranded, beta-clam protein, cellular retinoic acid-binding protein I (CRABP I), are favored in short peptide fragments, arguing that they are encoded by local interactions (K. S. Rotondi and L. M. Gierasch, Biochemistry, 2003, Vol. 42, pp. 7976-7985). In this paper we examine these turns in greater detail to dissect the specific local interactions responsible for their observed native conformational biases. Conformations of peptides corresponding to the turn III and IV fragments were examined under conditions designed to selectively disrupt stabilizing interactions, using pH variation, chaotrope addition, or mutagenesis to probe specific side-chain influences. We find that steric constraints imposed by excluded volume effects between near neighbor residues (i,i+2), favorable polar (i,i+2) interactions, and steric permissiveness of glycines are the principal factors accounting for the observed native bias in these turns. Longer-range stabilizing interactions across the beta-turns do not appear to play a significant role in turn stability in these short peptides, in contrast to their importance in hairpins. Additionally, our data add to a growing number of examples of the 3:5 type I turn with a beta-bulge as a class of turns with high propensity to form locally defined structure. Current work is directed at the interplay between the local sequence information in the turns and more long-range influences in the mechanism of folding of this predominantly beta-sheet protein.

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Section: Introductionmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Local sequence information in cellular retinoic acid‐binding protein I: Specific residue roles in β‐turns*

Rotondi

Gierasch

2003

Biopolymers

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“…Our early studies have focused on a heterologous protein expressed in E. coli, and we chose to use cellular retinoic acid-binding protein I (CRABP I) initially because of our extensive experience with the folding of this b-rich protein in vitro. [51][52][53][54][55][56] A clear advantage of using a non-E. coli protein is that folding can be studied without altering directly the cellular physiology by virtue of the function of the protein under study. CRABP I is also delicately balanced between successful folding and formation of aggregates, both in vitro and in vivo.…”

Section: The Full Monty: Exploring Protein Folding In Intact Cellsmentioning

confidence: 99%

A career pathway in protein folding: From model peptides to postreductionist protein science

Gierasch

2011

Protein Science

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This review discusses the inherent challenge of linking ''reductionist'' approaches to decipher the information encoded in protein sequences with burgeoning efforts to explore protein folding in native environments-''postreductionist'' approaches. Because the invitation to write this article came as a result of my selection to receive the 2010 Dorothy Hodgkin Award of the Protein Society, I use examples from my own work to illustrate the evolution from the reductionist to the postreductionist perspective. I am incredibly honored to receive the Hodgkin Award, but I want to emphasize that it is the combined effort, creativity, and talent of many students, postdoctoral fellows, and collaborators over several years that has led to any accomplishments on which this selection is based. Moreover, I do not claim to have unique insight into the topics discussed here; but this writing opportunity allows me to illustrate some threads in the evolution of protein folding research with my own experiences and to point out to those embarking on careers how the twists and turns in anyone's scientific path are influenced and enriched by the scientific context of our research. The path my own career has taken thus far has been shaped by the timing of discoveries in the field of protein science; together with our contemporaries, we become part of a knowledge evolution. In my own case, this has been an epoch of great discovery in protein folding and I feel very fortunate to have participated in it.

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“…In either case, they are expected to affect the stability and the folding kinetics of proteins, 2-10 and, in fact, β-hairpin formation is important for the folding of several proteins. 2,[11][12][13][14][15][16][17][18][19][20] The N-terminal domain of G3P (N2) (residues 102-205) of the gene-3-protein (G3P) of phage fd is a small autonomously folding protein. 21,22 At its top (in the orientation shown in Fig.…”

Section: Introductionmentioning

confidence: 99%

“…15 N hNOEs of wild-type N2′ (red) and the N2′ turn 3 variant QNGK variant (black) plotted as a function of the amino acid sequence. Errors are indicated as bars.…”

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confidence: 99%

Elimination of a cis-Proline-Containing Loop and Turn Optimization Stabilizes a Protein and Accelerates Its Folding

Jakob

Zierer

Weininger

et al. 2010

Journal of Molecular Biology

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Native structural propensity in cellular retinoic acid-binding protein I 64–88: the role of locally encoded structure in the folding of a β-barrel protein

Cited by 12 publications

References 56 publications

Local sequence information in cellular retinoic acid‐binding protein I: Specific residue roles in β‐turns*

Local sequence information in cellular retinoic acid‐binding protein I: Specific residue roles in β‐turns*

A career pathway in protein folding: From model peptides to postreductionist protein science

Elimination of a cis-Proline-Containing Loop and Turn Optimization Stabilizes a Protein and Accelerates Its Folding

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