α-Hairpin stability and folding of transmembrane segments

Khutorsky, V.

doi:10.1016/s0006-291x(02)02994-7

Cited by 8 publications

(7 citation statements)

References 21 publications

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“…Stability and folding of a-helices in non-polar environment was explored by MD simulations in case of several transmembrane peptides. [14] Here, a very fast dynamics of self-assembling into a-helical hairpin structure on the time scale of 100 ps was observed. Proteins are anchored in a membrane mostly as a helix bundle consisting of several parallel helices spanning the membrane.…”

Section: Folded Helical Structuresmentioning

confidence: 81%

“…Such a ''U''-shape structure of the type ''helix-turn-helix'' of two anti-parallel helical legs ( Figure 5) is also called the a-helical hairpin. [14] Figure 5 summarizes the representative structures from simulation of PA clustered in such a way that the values of any of three quantities H, R, and R g do not change more than AE 10%. At 303 K the double-leg hairpin was a principal arrangement of PA molecules (87.5% abundance), but a cluster of triple-leg hairpins was also established.…”

Section: Folded Helical Structuresmentioning

confidence: 99%

“…Such proteins traverse the cell membrane in a zigzag fashion and often fold in the form of a a-helical hairpin. This building block, consisting of two anti-parallel helices connected by a reverse turn, [14] is thought to be fundamental to integral membrane proteins and can be regarded as a supersecondary structural element. So far, the folding mechanism of proteins into a-helical hairpins has not been studied in detail and remains elusive.…”

Section: Introductionmentioning

confidence: 99%

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Folding of Polyalanine into Helical Hairpins

Palenčár

Bleha

2010

Macro Theory & Simulations

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The variation of the secondary structure and dimensions of long PA peptides was examined by means of all‐atom MD simulations. It was found that on cooling, instead of straight helices, hairpin‐like structures with two and three parallel helical legs were formed. The exclusive population of hairpins in PA at room temperature was proved by the bimodality of the distribution functions of the end‐to‐end distance and the radius of gyration. The helix‐turn‐helix motif revealed in PA simulations is pertinent for the structure of transmembrane proteins. The potential energy analysis showed a crucial role of the van der Waals forces in stabilization of the hairpins. It was underlined that this is a feature shared with folding of hydrocarbon chains, such as PE, into the crystal lamellae.

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Section: Folded Helical Structuresmentioning

confidence: 81%

Section: Folded Helical Structuresmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Folding of Polyalanine into Helical Hairpins

Palenčár

Bleha

2010

Macro Theory & Simulations

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“…In an aqueous medium, the hydrophobic effect will be prominent [42]. In water-poor conditions, like membranes, helices are frequently observed [43,44]. Finally, in vacuum conditions, the longer members (n ≥8) of the polyalanine based peptide series studied here assume helical structure in experiment [14,45,46].…”

Section: Introductionmentioning

confidence: 85%

Impact of Vibrational Entropy on the Stability of Unsolvated Peptide Helices with Increasing Length

2013

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Helices are a key folding motif in protein structure. The question of which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van-der-Waals-corrected density functional theory to address a part of this question in a bottom-up approach. We show how intrinsic helical structure is stabilized with length and temperature for a series of experimentally well-studied unsolvated alanine-based polypeptides, Ac-Alan-LysH(+). By exhaustively exploring the conformational space of these molecules, we find that helices emerge as the preferred structure in the length range n = 4-8 not just due to enthalpic factors (hydrogen bonds and their cooperativity, van der Waals dispersion interactions, electrostatics) but importantly also by a vibrational entropic stabilization over competing conformers at room temperature. The stabilization is shown to be due to softer low-frequency vibrational modes in helical conformers than in more compact ones. This observation is corroborated by including anharmonic effects explicitly through ab initio molecular dynamics and generalized by testing different terminations and considering larger helical peptide models.

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“…If so, this experimental finding would agree well with other results suggesting the importance of pairwise insertion of transmembrane a-helices in membrane protein folding. [74][75][76] In another study, bacteriorhodopsin was unfolded at different physiological temperatures ranging from 8-52 8C.…”

Section: Molecular Interactions Change Unfolding Pathwaysmentioning

confidence: 99%

From Valleys to Ridges: Exploring the Dynamic Energy Landscape of Single Membrane Proteins

et al. 2008

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Membrane proteins are involved in essential biological processes such as energy conversion, signal transduction, solute transport and secretion. All biological processes, also those involving membrane proteins, are steered by molecular interactions. Molecular interactions guide the folding and stability of membrane proteins, determine their assembly, switch their functional states or mediate signal transduction. The sequential steps of molecular interactions driving these processes can be described by dynamic energy landscapes. The conceptual energy landscape allows to follow the complex reaction pathways of membrane proteins while its modifications describe why and how pathways are changed. Single-molecule force spectroscopy (SMFS) detects, quantifies and locates interactions within and between membrane proteins. SMFS helps to determine how these interactions change with temperature, point mutations, oligomerization and the functional states of membrane proteins. Applied in different modes, SMFS explores the co-existence and population of reaction pathways in the energy landscape of the protein and thus reveals detailed insights into local mechanisms, determining its structural and functional relationships. Here we review how SMFS extracts the defining parameters of an energy landscape such as the barrier position, reaction kinetics and roughness with high precision.

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α-Hairpin stability and folding of transmembrane segments

Cited by 8 publications

References 21 publications

Folding of Polyalanine into Helical Hairpins

Folding of Polyalanine into Helical Hairpins

Impact of Vibrational Entropy on the Stability of Unsolvated Peptide Helices with Increasing Length

From Valleys to Ridges: Exploring the Dynamic Energy Landscape of Single Membrane Proteins

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