1
|
Zhuang Y, Bureau HR, Lopez C, Bucher R, Quirk S, Hernandez R. Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics. Biophys J 2021; 120:2009-2018. [PMID: 33775636 PMCID: PMC8204395 DOI: 10.1016/j.bpj.2021.03.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/03/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
The energetics and hydrogen bonding profiles of the helix-to-coil transition were found to be an additive property and to increase linearly with chain length, respectively, in alanine-rich α-helical peptides. A model system of polyalanine repeats was used to establish this hypothesis for the energetic trends and hydrogen bonding profiles. Numerical measurements of a synthesized polypeptide Ac-Y(AEAAKA)kF-NH2 and a natural α-helical peptide a2N (1-17) provide evidence of the hypothesis's generality. Adaptive steered molecular dynamics was employed to investigate the mechanical unfolding of all of these alanine-rich polypeptides. We found that the helix-to-coil transition is primarily dependent on the breaking of the intramolecular backbone hydrogen bonds and independent of specific side-chain interactions and chain length. The mechanical unfolding of the α-helical peptides results in a turnover mechanism in which a 310-helical structure forms during the unfolding, remaining at a near constant population and thereby maintaining additivity in the free energy. The intermediate partially unfolded structures exhibited polyproline II helical structure as previously seen by others. In summary, we found that the average force required to pull alanine-rich α-helical peptides in between the endpoints-namely the native structure and free coil-is nearly independent of the length or the specific primary structure.
Collapse
Affiliation(s)
- Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Hailey R Bureau
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Christine Lopez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Ryan Bucher
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | | | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland; Departments of Chemical and Biomolecular Engineering, and Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland.
| |
Collapse
|
2
|
Devaux F, Li X, Sluysmans D, Maurizot V, Bakalis E, Zerbetto F, Huc I, Duwez AS. Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding. Chem 2021. [DOI: 10.1016/j.chempr.2021.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
3
|
Bergues-Pupo AE, Lipowsky R, Vila Verde A. Unfolding mechanism and free energy landscape of single, stable, alpha helices at low pull speeds. SOFT MATTER 2020; 16:9917-9928. [PMID: 33030193 DOI: 10.1039/d0sm01166e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single alpha helices (SAHs) stable in isolated form are often found in motor proteins where they bridge functional domains. Understanding the mechanical response of SAHs is thus critical to understand their function. The quasi-static force-extension relation of a small number of SAHs is known from single-molecule experiments. Unknown, or still controversial, are the molecular scale details behind those observations. We show that the deformation mechanism of SAHs pulled from the termini at pull speeds approaching the quasi-static limit differs from that of typical helices found in proteins, which are stable only when interacting with other protein domains. Using molecular dynamics simulations with atomistic resolution at low pull speeds previously inaccessible to simulation, we show that SAHs start unfolding from the termini at all pull speeds we investigated. Unfolding proceeds residue-by-residue and hydrogen bond breaking is not the main event determining the barrier to unfolding. We use the molecular simulation data to test the cooperative sticky chain model. This model yields excellent fits of the force-extension curves and quantifies the distance, xE = 0.13 nm, to the transition state, the natural frequency of bond vibration, ν0 = 0.82 ns-1, and the height, V0 = 2.9 kcal mol-1, of the free energy barrier associated with the deformation of single residues. Our results demonstrate that the sticky chain model could advantageously be used to analyze experimental force-extension curves of SAHs and other biopolymers.
Collapse
Affiliation(s)
- Ana Elisa Bergues-Pupo
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Ana Vila Verde
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, Am Mühlenberg 1, 14476 Potsdam, Germany.
| |
Collapse
|
4
|
Sluysmans D, Willet N, Thevenot J, Lecommandoux S, Duwez AS. Single-molecule mechanical unfolding experiments reveal a critical length for the formation of α-helices in peptides. NANOSCALE HORIZONS 2020; 5:671-678. [PMID: 32226978 DOI: 10.1039/d0nh00036a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
α-Helix is the most predominant secondary structure in proteins and supports many functions in biological machineries. The conformation of the helix is dictated by many factors such as its primary sequence, intramolecular interactions, or the effect of the close environment. Several computational studies have proposed that there is a critical maximum length for the formation of intact compact helical structures, supporting the fact that most intact α-helices in proteins are constituted of a small number of amino acids. To obtain a detailed picture on the formation of α-helices in peptides and their mechanical stability, we have synthesized a long homopolypeptide of about 90 amino acids, poly(γ-benzyl-l-glutamate), and investigated its mechanical behaviour by AFM-based single-molecule force spectroscopy. The characteristic plateaus observed in the force-extension curves reveal the unfolding of a series of small helices (from 1 to 4) of about 20 amino acid residues connected to each other, rather than a long helix of 90 residues. Our results suggest the formation of a tertiary structure made of short helices with kinks, instead of an intact compact helical structure for sequences of more than 20 amino acid residues. To our knowledge, this is the first experimental evidence supporting the concept of a helical critical length previously proposed by several computational studies.
Collapse
Affiliation(s)
- Damien Sluysmans
- Molecular Systems Research Unit, University of Liège, Sart-Tilman B6a, 4000 Liège, Belgium.
| | - Nicolas Willet
- Molecular Systems Research Unit, University of Liège, Sart-Tilman B6a, 4000 Liège, Belgium. and Univ. Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France
| | - Julie Thevenot
- Univ. Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France
| | | | - Anne-Sophie Duwez
- Molecular Systems Research Unit, University of Liège, Sart-Tilman B6a, 4000 Liège, Belgium.
| |
Collapse
|
5
|
Affiliation(s)
- Korosh Torabi
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| |
Collapse
|
6
|
Abstract
Although stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit nontrivial behavior with a distinct plateau region. Here, we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the extension energy profile of its individual monomer subunits. Namely, if the effective monomer deformation energy as a function of its extension has a nonconvex (concave up) region, the stretched polymer chain separates into two phases: the weakly and strongly stretched monomers. Simplified planar and 3D polymer models are used to illustrate the basic principles of the proposed model. Specifically, we show rigorously that, when the secondary structure of a polymer is mostly caused by weak noncovalent interactions, the stretching is two phase, and the force-stretching diagram has the characteristic plateau. We then use realistic coarse-grained models to confirm the main findings and make direct connection to the microscopic structure of the monomers. We show in detail how the two-phase scenario is realized in the α-helix and DNA double helix. The predicted plateau parameters are consistent with single-molecules experiments. Detailed analysis of DNA stretching shows that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double helix extends at room temperature. The main strengths of the proposed theory are its generality and direct microscopic connection.
Collapse
Affiliation(s)
- Alexander V. Savin
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia; and
| | - Irina P. Kikot
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia; and
| | - Mikhail A. Mazo
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia; and
| | - Alexey V. Onufriev
- Departments of Computer Science and Physics, Virginia Tech, Blacksburg, VA 24061
| |
Collapse
|
7
|
Christiansen PL, Savin AV, Zolotaryuk AV. Lattice stretching bistability and dynamic heterogeneity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:046601. [PMID: 22680592 DOI: 10.1103/physreve.85.046601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 02/20/2012] [Indexed: 06/01/2023]
Abstract
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential (required to have a saturation branch) and a harmonic second-neighbor coupling. Under an external stretching applied to the chain ends, the intersite Morse-like potential results in the appearance of a double-well potential within each chain monomer, whereas the interaction between the second neighbors provides a homogeneous bistable (degenerate) ground state, at least within a certain part of the chain. As a result, different conformational changes occur in the chain under the external forcing. The transition regions between these conformations are described as topological solitons. With a strong second-neighbor interaction, the solitons describe the transition between the bistable ground states. However, the key point of the model is the appearance of a heterogenous structure, when the second-neighbor coupling is sufficiently weak. In this case, a part of the chain has short bonds with a single-well potential, whereas the complementary part admits strongly stretched bonds with a double-well potential. This case allows us to explain the existence of a plateau in the force-extension diagram for DNA and α-helix protein. Finally, the soliton dynamics are studied in detail.
Collapse
Affiliation(s)
- P L Christiansen
- Department of Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | |
Collapse
|
8
|
Yuan P, Zhao L, Liu N, Wei G, Wang Y, Auchterlonie GJ, Drennan J, Lu GQ, Zou J, Yu C. Evolution of Helical Mesostructures. Chemistry 2010; 16:1629-37. [DOI: 10.1002/chem.200902435] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pei Yuan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 220 Handan Road, Shanghai, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|