1
|
Effects of High-Pressure Treatments (Ultra-High Hydrostatic Pressure and High-Pressure Homogenization) on Bighead Carp (Aristichthys nobilis) Myofibrillar Protein Native State and Its Hydrolysate. FOOD BIOPROCESS TECH 2022. [DOI: 10.1007/s11947-022-02878-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
2
|
Sheng J, Chen W, Cui K, Li L. Polymer crystallization under external flow. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:036601. [PMID: 35060493 DOI: 10.1088/1361-6633/ac4d92] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
The general aspects of polymer crystallization under external flow, i.e., flow-induced crystallization (FIC) from fundamental theoretical background to multi-scale characterization and modeling results are presented. FIC is crucial for modern polymer processing, such as blowing, casting, and injection modeling, as two-third of daily-used polymers is crystalline, and nearly all of them need to be processed before final applications. For academics, the FIC is intrinsically far from equilibrium, where the polymer crystallization behavior is different from that in quiescent conditions. The continuous investigation of crystallization contributes to a better understanding on the general non-equilibrium ordering in condensed physics. In the current review, the general theories related to polymer nucleation under flow (FIN) were summarized first as a preliminary knowledge. Various theories and models, i.e., coil-stretch transition and entropy reduction model, are briefly presented together with the modified versions. Subsequently, the multi-step ordering process of FIC is discussed in detail, including chain extension, conformational ordering, density fluctuation, and final perfection of the polymer crystalline. These achievements for a thorough understanding of the fundamental basis of FIC benefit from the development of various hyphenated rheometer, i.e., rheo-optical spectroscopy, rheo-IR, and rheo-x-ray scattering. The selected experimental results are introduced to present efforts on elucidating the multi-step and hierarchical structure transition during FIC. Then, the multi-scale modeling methods are summarized, including micro/meso scale simulation and macroscopic continuum modeling. At last, we briefly describe our personal opinions related to the future directions of this field, aiming to ultimately establish the unified theory of FIC and promote building of the more applicable models in the polymer processing.
Collapse
Affiliation(s)
- Junfang Sheng
- National Synchrotron Radiation Laboratory, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Wei Chen
- National Synchrotron Radiation Laboratory, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Kunpeng Cui
- National Synchrotron Radiation Laboratory, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Liangbin Li
- National Synchrotron Radiation Laboratory, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, People's Republic of China
| |
Collapse
|
3
|
Noh G, Benetatos P. Tensile elasticity of a freely jointed chain with reversible hinges. SOFT MATTER 2021; 17:3333-3345. [PMID: 33630011 DOI: 10.1039/d1sm00053e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many biopolymers exhibit reversible conformational transitions within the chain, which affect their bending stiffness and their response to a stretching force. For example, double stranded DNA may have denatured "bubbles" of unzipped single strands which open and close randomly. In other polymers, the transitions may be due to the reversible attachment and detachment of ligands on ligand-receptor complexes along the backbone. Semiflexible bundles under tension formed by the reversible attachment of cross-linkers, on a coarse-grained level, exhibit similar behaviour. The simplest theoretical model which captures what the above mentioned systems have in common is a freely jointed chain (FJC) with reversible hinges. Each hinge can be open, as in the usual FJC, or closed forcing the adjacent segments to align (stretch). In this article, we analyse it in the Gibbs ensemble. Remarkably, even though the usual FJC in the thermodynamic limit exhibits ensemble equivalence, the reversible FJC exhibits ensemble inequivalence. Even though a mean field treatment suggests a continuous phase transition to a fully hinged state at a certain force, the generating function method ("necklace model") shows that there is no phase transition. However, there is a crossover between the two states with clearly different responses. In the low force (linear response) regime, the reversible FJC has higher tensile compliance than its usual counterpart. In contrast, in the strong force regime, the tensile compliance of the reversible FJC is much lower than that of the usual FJC.
Collapse
Affiliation(s)
- Geunho Noh
- Department of Physics, Kyungpook National University, Bukgu, 80 Daehakro, Daegu 41566, Korea.
| | | |
Collapse
|
4
|
Chen X, Meng L, Zhang W, Ye K, Xie C, Wang D, Chen W, Nan M, Wang S, Li L. Frustrating Strain-Induced Crystallization of Natural Rubber with Biaxial Stretch. ACS APPLIED MATERIALS & INTERFACES 2019; 11:47535-47544. [PMID: 31750643 DOI: 10.1021/acsami.9b15865] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The supreme mechanical performance of natural rubber (NR) is commonly attributed to strain-induced crystallization (SIC). The SIC of NR during uniaxial stretch has been extensively investigated, whereas that under multiaxial deformation has been rarely reported, which is close to real service conditions (i.e., tire). In this work, the crystallization behavior of NR under biaxial stretch was studied with in situ synchrotron radiation wide-angle X-ray diffraction in combination with a custom-built biaxial stretch machine. It is observed that biaxial stretch frustrates the SIC of NR: within λx/λy < 1.6, where λx and λy are stretch ratios of two mutually perpendicular axes, no crystallization emerges even under large drawing ratio until sample fracture at ambient temperature. This finding challenges the common wisdom of the self-reinforcement mechanism of SIC in NR under multiaxial deformation in real service conditions. A theoretical SIC model is proposed, which can decouple the contributions of conformational entropy reduction ΔSf and amorphous chain orientation f to final Gibbs free energy change (ΔG) during multiaxial deformation. This model quantitatively renders a reproduction of the crystallinity during the biaxial stretch, which is well consistent with experimental results and can be further generalized for flow-induced crystallization of semicrystalline polymers.
Collapse
Affiliation(s)
- Xiaowei Chen
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Lingpu Meng
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Wenwen Zhang
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Ke Ye
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Chun Xie
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Daoliang Wang
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Wei Chen
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Mingjian Nan
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Shihao Wang
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Liangbin Li
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry , University of Science and Technology of China , Hefei 230026 , China
| |
Collapse
|
5
|
Tang X, Chen W, Li L. The Tough Journey of Polymer Crystallization: Battling with Chain Flexibility and Connectivity. Macromolecules 2019. [DOI: 10.1021/acs.macromol.8b02725] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaoliang Tang
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Wei Chen
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Liangbin Li
- National Synchrotron Radiation Lab, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, China
| |
Collapse
|
6
|
Yue K, Liu G, Feng X, Li L, Lotz B, Cheng SZD. A few rediscovered and challenging topics in polymer crystals and crystallization. POLYMER CRYSTALLIZATION 2018. [DOI: 10.1002/pcr2.10053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kan Yue
- South China Advanced Institute for Soft Matter Science and Technology, South China University of Technology Guangzhou China
| | - Gengxin Liu
- Center for Advanced Low‐dimensional Materials Donghua University Shanghai China
| | - Xueyan Feng
- College of Polymer Science and Polymer Engineering, The University of Akron Akron Ohio
| | - Liangbin Li
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry University of Science and Technology of China Hefei China
| | - Bernard Lotz
- Institut Charles Sadron, CNRS‐Universite de Strasbourg Strasbourg France
| | - Stephen Z. D. Cheng
- South China Advanced Institute for Soft Matter Science and Technology, South China University of Technology Guangzhou China
- College of Polymer Science and Polymer Engineering, The University of Akron Akron Ohio
| |
Collapse
|
7
|
Tang X, Yang J, Tian F, Xu T, Xie C, Chen W, Li L. Flow-induced density fluctuation assisted nucleation in polyethylene. J Chem Phys 2018; 149:224901. [PMID: 30553254 DOI: 10.1063/1.5054273] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Xiaoliang Tang
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Junsheng Yang
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
- Computational Physics Key Laboratory of Sichuan Province, Yibin University, Yibin, China
| | - Fucheng Tian
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Tingyu Xu
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Chun Xie
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Wei Chen
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Liangbin Li
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| |
Collapse
|
8
|
Xie C, Tang X, Yang J, Xu T, Tian F, Li L. Stretch-Induced Coil–Helix Transition in Isotactic Polypropylene: A Molecular Dynamics Simulation. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00325] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Chun Xie
- National Synchrotron Radiation Lab, CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Xiaoliang Tang
- National Synchrotron Radiation Lab, CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Junsheng Yang
- National Synchrotron Radiation Lab, CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
- Computational Physics Key Laboratory of Sichuan Province, Yibin University, Yibin, China
| | - Tingyu Xu
- National Synchrotron Radiation Lab, CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Fucheng Tian
- National Synchrotron Radiation Lab, CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| | - Liangbin Li
- National Synchrotron Radiation Lab, CAS Key Laboratory of Soft Matter Chemistry, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, Hefei, China
| |
Collapse
|
9
|
Cui K, Ma Z, Tian N, Su F, Liu D, Li L. Multiscale and Multistep Ordering of Flow-Induced Nucleation of Polymers. Chem Rev 2018; 118:1840-1886. [DOI: 10.1021/acs.chemrev.7b00500] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kunpeng Cui
- National
Synchrotron Radiation Laboratory, Chinese Academy of Sciences Key
Laboratory of Soft Matter Chemistry, and Anhui Provincial Engineering
Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, 96 Jinzhai Road, Baohe District, Hefei 230026, People’s Republic of China
| | - Zhe Ma
- Tianjin
Key Laboratory of Composite and Functional Materials, School of Materials
Science and Engineering, Tianjin University, 92 Weijin Road,
Nankai District, Tianjin 300072, People’s Republic of China
| | - Nan Tian
- Ministry
of Education Key Laboratory of Space Applied Physics and Chemistry
and Shanxi Key Laboratory of Macromolecular Science and Technology,
School of Science, Northwestern Polytechnical University, 127 Youyi
West Road, District Beilin, Xi’an 710072, People’s Republic of China
| | - Fengmei Su
- National
Synchrotron Radiation Laboratory, Chinese Academy of Sciences Key
Laboratory of Soft Matter Chemistry, and Anhui Provincial Engineering
Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, 96 Jinzhai Road, Baohe District, Hefei 230026, People’s Republic of China
| | - Dong Liu
- Key
Laboratory of Neutron Physics and Institute of Nuclear Physics and
Chemistry, China Academy of Engineering Physics, 64 Mianshan
Road, Mianyang, Sichuan 621999, People’s Republic of China
| | - Liangbin Li
- National
Synchrotron Radiation Laboratory, Chinese Academy of Sciences Key
Laboratory of Soft Matter Chemistry, and Anhui Provincial Engineering
Laboratory of Advanced Functional Polymer Film, University of Science and Technology of China, 96 Jinzhai Road, Baohe District, Hefei 230026, People’s Republic of China
| |
Collapse
|
10
|
Yang J, Tang X, Wang Z, Xu T, Tian F, Ji Y, Li L. Coupling between intra- and inter-chain orderings in flow-induced crystallization of polyethylene: A non-equilibrium molecular dynamics simulation study. J Chem Phys 2017; 146:014901. [DOI: 10.1063/1.4973382] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Junsheng Yang
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
- Computational Physics Key Laboratory of Sichuan Province, Yibin University, Yibin, China
| | - Xiaoliang Tang
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
| | - Zhen Wang
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
| | - Tingyu Xu
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
| | - Fucheng Tian
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
| | - Youxin Ji
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
| | - Liangbin Li
- National Synchrotron Radiation Lab and CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
| |
Collapse
|
11
|
Lavalle P, Boulmedais F, Schaaf P, Jierry L. Soft-Mechanochemistry: Mechanochemistry Inspired by Nature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7265-7276. [PMID: 27396617 DOI: 10.1021/acs.langmuir.6b01768] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cells and bacteria use mechanotransduction processes to transform a mechanical force into a chemical/biochemical response. The area of chemistry where chemical reactions are induced by mechanical forces is called mechanochemistry. Over the last few years, chemists developed force-induced reactions affecting covalent bonds in molecules under tension which requires high energy input and/or high intensity forces. In contrast, in nature, mechanotransduction processes take place with forces of much weaker intensity and much less demanding energy. They are mainly based on protein conformational changes or changes in supramacromolecular architectures. Mechanochemistry based on such low-energy-demanding processes and which does not affect chemical bonds can be called soft-mechanochemistry. In this feature article, we first discuss some examples of soft-mechanochemistry processes encountered in nature, in particular, cryptic sites, allowing us to define more precisely the concepts underlying soft-mechanochemistry. A series of examples, developed over the past few years, of chemomechanoresponsive systems based on soft-mechanochemistry principles are given. We describe, in particular, cryptic site surfaces, enzymatically active films whose activity can be modulated by stretching and films where stretching induces changes in their fluorescence properties. Finally, we give our view of the future of soft-mechanochemistry.
Collapse
Affiliation(s)
- Philippe Lavalle
- Unité INSERM U1121, Biomaterials and Bioengineering, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Fédération de Médecine Translationnelle de Strasbourg (FMTS), and Fédération des Matériaux et Nanoscience d'Alsace (FMNA), Université de Strasbourg , 8 rue Saint Elisabeth, 67000 Strasbourg, France
| | - Fouzia Boulmedais
- Institut Charles Sadron, Centre National de la Recherche Scientifique, Université de Strasbourg , 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Pierre Schaaf
- Unité INSERM U1121, Biomaterials and Bioengineering, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Fédération de Médecine Translationnelle de Strasbourg (FMTS), and Fédération des Matériaux et Nanoscience d'Alsace (FMNA), Université de Strasbourg , 8 rue Saint Elisabeth, 67000 Strasbourg, France
- Institut Charles Sadron, Centre National de la Recherche Scientifique, Université de Strasbourg , 23 rue du Loess, 67034 Strasbourg Cedex 2, France
- University of Strasbourg Institute of Advanced Study , 5 allée du Général Rouvillois, 67083 Strasbourg, France
| | - Loïc Jierry
- Institut Charles Sadron, Centre National de la Recherche Scientifique, Université de Strasbourg , 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| |
Collapse
|
12
|
Zahouani S, Chaumont A, Senger B, Boulmedais F, Schaaf P, Jierry L, Lavalle P. Stretch-Induced Helical Conformations in Poly(l-lysine)/Hyaluronic Acid Multilayers. ACS APPLIED MATERIALS & INTERFACES 2016; 8:14958-14965. [PMID: 26646202 DOI: 10.1021/acsami.5b08302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We investigate the effect of stretching on the secondary structure of cross-linked poly(l-lysine)/hyaluronic acid (PLL/HA) multilayers. We show that stretching these films induces changes in the secondary structure of PLL chains. Our results suggest that not only α- but also 310-helices might form in the film under stretching. Such 310-helices have never been observed for PLL so far. These changes of the secondary structure of PLL are reversible, i.e., when returning to the nonstretched state one recovers the initial film structure. Using molecular dynamics simulations of chains composed of 20 l-lysine residues (PLL20), we find that these chains never adopt a helical conformation in water. In contrast, when the end-to-end distance of the chains is restrained to values smaller than the mean end-to-end distance of free chains, a distance domain rarely explored by the free chains, helical conformations become accessible. Moreover, the formation of not only α- but also 310-helices is predicted by the simulations. These results suggest that the change of the end-to-end distance of PLL chains in the stretched film is at the origin of the helix formation.
Collapse
Affiliation(s)
- Sarah Zahouani
- Institut National de la Santé et de la Recherche Médicale, INSERM Unité 1121 , 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg , 8 rue Sainte Elisabeth, 67000 Strasbourg, France
| | - Alain Chaumont
- Faculté de Chimie, UMR 7177, Université de Strasbourg , 1 rue Blaise Pascal, 67008 Strasbourg Cedex, France
| | - Bernard Senger
- Institut National de la Santé et de la Recherche Médicale, INSERM Unité 1121 , 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg , 8 rue Sainte Elisabeth, 67000 Strasbourg, France
| | - Fouzia Boulmedais
- Institut Charles Sadron, CNRS UPR 22 , 23 rue du Lœss, 67034 Strasbourg Cedex, France
- University of Strasbourg Institute of Advanced Study , 5 allée du Général Rouvillois, 67083 Strasbourg Cedex, France
| | - Pierre Schaaf
- Institut National de la Santé et de la Recherche Médicale, INSERM Unité 1121 , 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg , 8 rue Sainte Elisabeth, 67000 Strasbourg, France
- Institut Charles Sadron, CNRS UPR 22 , 23 rue du Lœss, 67034 Strasbourg Cedex, France
- University of Strasbourg Institute of Advanced Study , 5 allée du Général Rouvillois, 67083 Strasbourg Cedex, France
| | - Loïc Jierry
- Institut Charles Sadron, CNRS UPR 22 , 23 rue du Lœss, 67034 Strasbourg Cedex, France
- University of Strasbourg Institute of Advanced Study , 5 allée du Général Rouvillois, 67083 Strasbourg Cedex, France
| | - Philippe Lavalle
- Institut National de la Santé et de la Recherche Médicale, INSERM Unité 1121 , 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg , 8 rue Sainte Elisabeth, 67000 Strasbourg, France
| |
Collapse
|
13
|
Wang Z, Ma Z, Li L. Flow-Induced Crystallization of Polymers: Molecular and Thermodynamic Considerations. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b02688] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zhen Wang
- National
Synchrotron Radiation Lab, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
| | - Zhe Ma
- School
of Materials Science and Engineering, Tianjin University, Tianjin, China
| | - Liangbin Li
- National
Synchrotron Radiation Lab, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
| |
Collapse
|
14
|
Ronsin O, Caroli C, Baumberger T. Glass-like dynamics of the strain-induced coil/helix transition on a permanent polymer network. J Chem Phys 2016; 144:064904. [DOI: 10.1063/1.4941456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
15
|
Xiao S, Gräter F. Molecular basis of the mechanical hierarchy in myomesin dimers for sarcomere integrity. Biophys J 2015; 107:965-73. [PMID: 25140432 PMCID: PMC4142248 DOI: 10.1016/j.bpj.2014.06.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/26/2014] [Accepted: 06/16/2014] [Indexed: 01/08/2023] Open
Abstract
Myomesin is one of the most important structural molecules constructing the M-band in the force-generating unit of striated muscle, and a critical structural maintainer of the sarcomere. Using molecular dynamics simulations, we here dissect the mechanical properties of the structurally known building blocks of myomesin, namely α-helices, immunoglobulin (Ig) domains, and the dimer interface at myomesin's 13th Ig domain, covering the mechanically important C-terminal part of the molecule. We find the interdomain α-helices to be stabilized by the hydrophobic interface formed between the N-terminal half of these helices and adjacent Ig domains, and, interestingly, to show a rapid unfolding and refolding equilibrium especially under low axial forces up to ∼ 15 pN. These results support and yield atomic details for the notion of recent atomic-force microscopy experiments, namely, that the unique helices inserted between Ig domains in myomesin function as elastomers and force buffers. Our results also explain how the C-terminal dimer of two myomesin molecules is mechanically outperforming the helices and Ig domains in myomesin and elsewhere, explaining former experimental findings. This study provides a fresh view onto how myomesin integrates elastic helices, rigid immunoglobulin domains, and an extraordinarily resistant dimer into a molecular structure, to feature a mechanical hierarchy that represents a firm and yet extensible molecular anchor to guard the stability of the sarcomere.
Collapse
Affiliation(s)
- Senbo Xiao
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Chinese Academy of Sciences-Max-Planck-Society Partner Institute and Key Laboratory for Computational Biology, Shanghai, China; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
16
|
Sharma GP, Reshetnyak YK, Andreev OA, Karbach M, Müller G. Coil-helix transition of polypeptide at water-lipid interface. JOURNAL OF STATISTICAL MECHANICS (ONLINE) 2015; 2015:P01034. [PMID: 31456824 PMCID: PMC6711616 DOI: 10.1088/1742-5468/2015/01/p01034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an α-helix conformation. The polypeptide is assumed to be adsorbed to the interface between a polar and a non-polar environment such as realized by water and the lipid bilayer of a membrane. The interfacial coil-helix transformation is the first stage in the folding process of helical membrane proteins. Depending on the values of model parameters, the conformation changes as a crossover, a discontinuous transition, or a continuous transition with helicity in the role of order parameter. Our model is constructed as a system of statistically interacting quasiparticles that are activated from the helix pseudo-vacuum. The particles represent links between adjacent residues in coil conformation that form a self-avoiding random walk in two dimensions. Explicit results are presented for helicity, entropy, heat capacity, and the average numbers and sizes of sboth coil and helix segments.
Collapse
Affiliation(s)
- Ganga P Sharma
- Department of Physics, University of Rhode Island, Kingston RI 02881, USA
| | - Yana K Reshetnyak
- Department of Physics, University of Rhode Island, Kingston RI 02881, USA
| | - Oleg A Andreev
- Department of Physics, University of Rhode Island, Kingston RI 02881, USA
| | - Michael Karbach
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Gerhard Müller
- Department of Physics, University of Rhode Island, Kingston RI 02881, USA
| |
Collapse
|
17
|
Abstract
We present a novel tunable thermoresponsive gelatin nanogel that shows a volume transition at ∼32 °C. A thermally induced volume reduction of more than 30× is observed due to the helix to random coil transition of gelatin chains confined in the nanogels. The physical process and key factors influencing thermoresponsive properties are investigated using dynamic light scattering (DLS), transmission electron microscopy (TEM), and polarimetry. The thermoresponsive properties of this nanogel can be exploited in the development of new types of stimuli-responsive, biomedically relevant materials based on natural polymers.
Collapse
Affiliation(s)
- Sahil Sandesh Gandhi
- Chemical Physics Interdisciplinary
Program and Liquid Crystal Institute, Kent State University, P.O. Box 5190, Kent, Ohio 44242, United States
| | - Huan Yan
- Chemical Physics Interdisciplinary
Program and Liquid Crystal Institute, Kent State University, P.O. Box 5190, Kent, Ohio 44242, United States
| | - Chanjoong Kim
- Chemical Physics Interdisciplinary
Program and Liquid Crystal Institute, Kent State University, P.O. Box 5190, Kent, Ohio 44242, United States
| |
Collapse
|
18
|
Zhang Y, Sagui C. The gp41659–671 HIV-1 Antibody Epitope: A Structurally Challenging Small Peptide. J Phys Chem B 2013; 118:69-80. [DOI: 10.1021/jp409355r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yuan Zhang
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
- Center
for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Celeste Sagui
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
- Center
for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
19
|
Badasyan AV, Tonoyan SA, Mamasakhlisov YS, Giacometti A, Benight AS, Morozov VF. Competition for hydrogen-bond formation in the helix-coil transition and protein folding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:051903. [PMID: 21728568 DOI: 10.1103/physreve.83.051903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Indexed: 05/31/2023]
Abstract
The problem of the helix-coil transition of biopolymers in explicit solvents, such as water, with the ability for hydrogen bonding with a solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress, or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.
Collapse
Affiliation(s)
- A V Badasyan
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Venezia, Italy.
| | | | | | | | | | | |
Collapse
|
20
|
Tensile Mechanics of α-Helical Coil Springs. Biopolymers 2010. [DOI: 10.1007/12_2009_41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
21
|
Makarov DE. A theoretical model for the mechanical unfolding of repeat proteins. Biophys J 2009; 96:2160-7. [PMID: 19289042 DOI: 10.1016/j.bpj.2008.12.3899] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 11/26/2008] [Accepted: 12/08/2008] [Indexed: 11/18/2022] Open
Abstract
We consider the mechanical stretching of a polypeptide chain formed by multiple interacting repeats. The folding thermodynamics and the interactions among the repeats are described by the Ising model. Unfolded repeats act as soft entropic springs, whereas folded repeats respond to a force as stiffer springs. We show that the resulting force-extension curve may exhibit a pronounced force maximum corresponding to the unfolding of the first repeat. This event is followed by the unfolding of the remaining repeats, which takes place at a lower force. As the protein extension is increased, the force-extension curve of a sufficiently long repeat protein displays a plateau, where the force remains nearly constant and the protein unfolds sequentially so that the number of unfolded repeats is proportional to the extension. Such a sequential mechanical unfolding mechanism is displayed even by the repeat proteins whose thermal denaturation is highly cooperative, provided that they are long enough. By contrast, the unfolding of short repeat progressions can be cooperative.
Collapse
Affiliation(s)
- Dmitrii E Makarov
- Department of Chemistry and Biochemistry and Institute for Theoretical Chemistry, University of Texas at Austin, Austin, Texas, USA.
| |
Collapse
|
22
|
Geng Y, Wang G, Cong Y, Bai L, Li L, Yang C. Shear-Induced Nucleation and Growth of Long Helices in Supercooled Isotactic Polypropylene. Macromolecules 2009. [DOI: 10.1021/ma9004567] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yong Geng
- Department of Physics and Electrons, Ludong University, Yantai, China
- National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Guanglin Wang
- National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Yuanhua Cong
- National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Liangui Bai
- National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Liangbin Li
- National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Chuanlu Yang
- Department of Physics and Electrons, Ludong University, Yantai, China
| |
Collapse
|
23
|
Zegarra FC, Peralta GN, Coronado AM, Gao YQ. Free energies and forces in helix-coil transition of homopolypeptides under stretching. Phys Chem Chem Phys 2009; 11:4019-24. [PMID: 19440631 DOI: 10.1039/b820021a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show here that constant velocity steered molecular dynamics (SMD) simulations of alpha-helices in a vacuum present a well defined plateau in the force-extension relationship for homopolypeptides having more than (approximately) twenty residues. With the processes being far away from equilibrium, the energies strongly depend on the stretching velocity. Importantly, for a given velocity variation, the energy variation depends also on the helix sequence. Additionally, our observations show that homopolypeptides made of ten different amino acids (Ala, Cys, Gln, Ile, Leu, Met, Phe, Ser, Thr and Val) present a linear helix-coil transition.
Collapse
Affiliation(s)
- Fabio C Zegarra
- Facultad de Ingeniería Mecánica, Universidad Nacional de Ingeniería, Lima, Peru
| | | | | | | |
Collapse
|
24
|
An H, Li X, Geng Y, Wang Y, Wang X, Li L, Li Z, Yang C. Shear-Induced Conformational Ordering, Relaxation, and Crystallization of Isotactic Polypropylene. J Phys Chem B 2008; 112:12256-62. [DOI: 10.1021/jp802511b] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haining An
- National Synchrotron Radiation Laboratory and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and Department of Physics and Electrons, Ludong University, Yantai, China
| | - Xiangyang Li
- National Synchrotron Radiation Laboratory and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and Department of Physics and Electrons, Ludong University, Yantai, China
| | - Yong Geng
- National Synchrotron Radiation Laboratory and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and Department of Physics and Electrons, Ludong University, Yantai, China
| | - Yunlong Wang
- National Synchrotron Radiation Laboratory and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and Department of Physics and Electrons, Ludong University, Yantai, China
| | - Xiao Wang
- National Synchrotron Radiation Laboratory and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and Department of Physics and Electrons, Ludong University, Yantai, China
| | - Liangbin Li
- National Synchrotron Radiation Laboratory and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and Department of Physics and Electrons, Ludong University, Yantai, China
| | - Zhongming Li
- National Synchrotron Radiation Laboratory and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and Department of Physics and Electrons, Ludong University, Yantai, China
| | - Chuanlu Yang
- National Synchrotron Radiation Laboratory and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China, College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and Department of Physics and Electrons, Ludong University, Yantai, China
| |
Collapse
|
25
|
An H, Zhao B, Ma Z, Shao C, Wang X, Fang Y, Li L, Li Z. Shear-Induced Conformational Ordering in the Melt of Isotactic Polypropylene. Macromolecules 2007. [DOI: 10.1021/ma071021h] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haining An
- College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Baijin Zhao
- College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Zhe Ma
- College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Chunguang Shao
- College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Xiao Wang
- College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Yapeng Fang
- College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Liangbin Li
- College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Zhongming Li
- College of Polymer Science and Engineering and State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China, and National Synchrotron Radiation Lab and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, China
| |
Collapse
|
26
|
Seol Y, Skinner GM, Visscher K, Buhot A, Halperin A. Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking. PHYSICAL REVIEW LETTERS 2007; 98:158103. [PMID: 17501388 DOI: 10.1103/physrevlett.98.158103] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Indexed: 05/15/2023]
Abstract
We have found strong supporting evidence for the helical structures of single-stranded nucleic acids by stretching individual molecules of polyadenylic acid [poly(A)] and polycytidylic acid [poly(C)]. Analyzing the force versus extension data using a two-state elastic model in which random-coil domains alternate with rigid helical domains allows one to extract the thermodynamic and structural properties. In addition, it also yields moderate to low cooperativity of the helix-coil transition for poly(A) and poly(C), respectively.
Collapse
Affiliation(s)
- Yeonee Seol
- Department of Physics, University of Arizona, Arizona 85721, USA
| | | | | | | | | |
Collapse
|
27
|
Nowak C, Rostiashvili VG, Vilgis TA. Globular structures of a helix-coil copolymer: Self-consistent treatment. J Chem Phys 2007; 126:034902. [PMID: 17249898 DOI: 10.1063/1.2403868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A self-consistent-field theory was developed in the grand canonical ensemble formulation to study transitions in a helix-coil multiblock globule. Helical and coil parts are treated as stiff rods and self-avoiding walks of variable lengths correspondingly. The resulting field theory takes, in addition to the conventional Zimm-Bragg, [J. Chem. Phys. 31, 526 (1959)] parameters, also three-dimensional interaction terms into account. The appropriate differential equations which determine the self-consistent fields were solved numerically with finite element method. Three different phase states are found: open chain, amorphous globule, and nematic liquid-crystalline (LC) globule. The LC-globule formation is driven by the interplay between the hydrophobic helical segment attraction and the anisotropic globule surface energy of an entropic nature. The full phase diagram of the helix-coil copolymer was calculated and thoroughly discussed. The suggested theory shows a clear interplay between secondary and tertiary structures in globular homopolypeptides.
Collapse
Affiliation(s)
- C Nowak
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | | | | |
Collapse
|
28
|
Abstract
We review the force-extension behavior of polymers collapsed in poor solvent, modified to include the effects of semiflexibility and considered for globules with "ordered" and "disordered" internal structures. A series of ordered globules is used as a model for the unbinding of a disordered globule beneath its glass transition and for multiple-repeat proteins such as the poly-Ig-domain titin used in atomic force microscopy studies. These single-chain results form the foundation for the treatment of cross-linked networks of globular polymers.
Collapse
Affiliation(s)
- A Craig
- Cavendish Laboratory, University of Cambridge Madingley Road, Cambridge, CB3 OHE, United Kingdom
| | | |
Collapse
|
29
|
Chakrabarti B, Levine AJ. Nonlinear elasticity of an alpha-helical polypeptide: Monte Carlo studies. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:031903. [PMID: 17025663 DOI: 10.1103/physreve.74.031903] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 06/12/2006] [Indexed: 05/12/2023]
Abstract
We report on Monte Carlo studies of the elastic properties of the helix-coil wormlike chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising-like) variable that controls the local chain bending modulus. We characterize the nonlinear elastic properties of these molecules including their response to applied tensile forces and bending torques both individually and in combination. We find a pronounced effect of applied torque on the extensional compliance of the molecule and a similar effect of tension on the bending compliance. Finally we speculate that the strongly nonlinear response of alpha-helical polypeptides to combinations of torque and force plays a role in allosteric transitions in proteins.
Collapse
|
30
|
Craig A, Terentjev EM. Auxiliary Field Theory of Polymers with Intrinsic Curvature. Macromolecules 2006. [DOI: 10.1021/ma060159h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Craig
- Cavendish Laboratory, J. J. Thomson Road, Cambridge, U.K., CB3 0HE
| | - E. M. Terentjev
- Cavendish Laboratory, J. J. Thomson Road, Cambridge, U.K., CB3 0HE
| |
Collapse
|
31
|
Ireta J, Neugebauer J, Scheffler M, Rojo A, Galván M. Structural Transitions in the Polyalanine α-Helix under Uniaxial Strain. J Am Chem Soc 2005; 127:17241-4. [PMID: 16332072 DOI: 10.1021/ja053538j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We analyzed the response to strain of an infinite polyalanine chain in the alpha-helical conformation using density functional theory. Under compressive strain the alpha-helix is found to undergo structural transitions to a pi-helix when the length of the helix is reduced by more than 10%. Under tensile strain the structure changes into a 3(10)-helix when the length is stretched by more than 10%. Our analysis of these transitions shows that they proceed essentially in two steps: At first there is mainly a length change, and only with some delay the helix twist adjusts.
Collapse
Affiliation(s)
- Joel Ireta
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin-Dahlem, Germany.
| | | | | | | | | |
Collapse
|
32
|
Courty S, Gornall JL, Terentjev EM. Mechanically induced helix-coil transition in biopolymer networks. Biophys J 2005; 90:1019-27. [PMID: 16239334 PMCID: PMC1367088 DOI: 10.1529/biophysj.105.067090] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The quasi-equilibrium evolution of the helical fraction occurring in a biopolymer network (gelatin gel) under an applied stress has been investigated by observing modulation in its optical activity. Its variation with the imposed chain extension is distinctly nonmonotonic and corresponds to the transition of initially coiled strands to induced left-handed helices. The experimental results are in qualitative agreement with theoretical predictions of helices induced on chain extension. This new effect of mechanically stimulated helix-coil transition has been studied further as a function of the elastic properties of the polymer network: crosslink density and network aging.
Collapse
Affiliation(s)
- Sebastien Courty
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | | | | |
Collapse
|
33
|
Courty S, Gornall JL, Terentjev EM. Induced helicity in biopolymer networks under stress. Proc Natl Acad Sci U S A 2005; 102:13457-60. [PMID: 16150704 PMCID: PMC1224673 DOI: 10.1073/pnas.0506864102] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
By combining dynamic mechanical and optical measurements in probing the internal structure of a biopolymer network (gelatin gel), we studied the quasi-equilibrium evolution of helical content as a function of the applied stress. Assuming that the net optical activity is proportional to the concentration of secondary helices of collagen chains, and assuming that affine mechanical deformation, we find a nonmonotonic relationship between the helical domains and an imposed deformation. The results are in qualitative agreement with theoretical predictions of alpha-helices induced by chain end-to-end stretching, and give a consistent picture of mechanically stimulated helix-coil transition in networks of denatured polypeptides.
Collapse
Affiliation(s)
- S Courty
- Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom
| | | | | |
Collapse
|
34
|
Chakrabarti B, Levine AJ. Nonlinear elasticity of an alpha -helical polypeptide. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 71:031905. [PMID: 15903457 DOI: 10.1103/physreve.71.031905] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Indexed: 05/02/2023]
Abstract
We study a minimal extension of the wormlike chain model to describe polypeptides having alpha-helical secondary structure. In this model the presence or absence of secondary structure enters as a scalar variable that controls the local chain bending modulus. Using this model we compute the extensional compliance of an alpha-helix under tensile stress, the bending compliance of the molecule under externally imposed torques, and the nonlinear interaction of such torques and forces on the molecule. We find that, due to coupling of the "internal" secondary structure variables to the conformational degrees of freedom of the polymer, the molecule has a highly nonlinear response to applied stress and force couples. In particular we demonstrate a sharp lengthening transition under applied force and a buckling transition under applied torque. Finally, we speculate that the inherent bistability of the molecule may underlie protein conformational change in vivo.
Collapse
|
35
|
Li L, de Jeu WH. Flow-induced mesophases in crystallizable polymers. ADVANCES IN POLYMER SCIENCE 2005. [DOI: 10.1007/b107175] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
36
|
Affiliation(s)
- Vikas Varshney
- The Maurice Morton Institute of Polymer Science, The University of Akron, Akron, Ohio 44325-3909
| | - Gustavo A. Carri
- The Maurice Morton Institute of Polymer Science, The University of Akron, Akron, Ohio 44325-3909
| |
Collapse
|
37
|
Toda M, Tanaka F. Optical Resolution of Chiral Molecules by Stretching Hydrogen-Bonding Helical Polymers. Macromolecules 2004. [DOI: 10.1021/ma048184f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Masatoshi Toda
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Fumihiko Tanaka
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| |
Collapse
|
38
|
Varshney V, Dirama TE, Sen TZ, Carri GA. A Minimal Model for the Helix−Coil Transition of Wormlike Polymers. Insights from Monte Carlo Simulations and Theoretical Implications. Macromolecules 2004. [DOI: 10.1021/ma049338u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vikas Varshney
- The Maurice Morton Institute of Polymer Science, The University of Akron, Akron, Ohio 44325-3909
| | - Taner E. Dirama
- The Maurice Morton Institute of Polymer Science, The University of Akron, Akron, Ohio 44325-3909
| | - Taner Z. Sen
- The Maurice Morton Institute of Polymer Science, The University of Akron, Akron, Ohio 44325-3909
| | - Gustavo A. Carri
- The Maurice Morton Institute of Polymer Science, The University of Akron, Akron, Ohio 44325-3909
| |
Collapse
|
39
|
Chen Y, Zhang Q, Ding J. A coarse-grained model and associated lattice Monte Carlo simulation of the coil–helix transition of a homopolypeptide. J Chem Phys 2004; 120:3467-74. [PMID: 15268504 DOI: 10.1063/1.1640667] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new coarse-grained lattice model neglecting atomic details is proposed for the coil-helix transition and a new physical parameter is suggested to characterize a helical structure. In our model, each residue is represented by eight lattice sites, and side groups are not considered explicitly. Chirality and hydrogen bonding are taken into consideration in addition to chain connectivity and the excluded volume effect. Through a dynamic Monte Carlo simulation, the physical properties of the coil-helix transition of a single homopolypeptide have been produced successfully within a short computing time on the PC. We also examined the effects of the variation of chain configurations including chain size and chain shape, etc. A spatial correlation function has been introduced in order to characterize periodicity of a helical chain in a simple way. A propagation parameter and a nucleation parameter have also been calculated, which compares favorably with the results of the Zimm-Bragg theory for the coil-helix transition.
Collapse
Affiliation(s)
- Yantao Chen
- Department of Macromolecular Science, Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | | | | |
Collapse
|
40
|
|
41
|
Storm C, Nelson PC. Theory of high-force DNA stretching and overstretching. PHYSICAL REVIEW E 2003; 67:051906. [PMID: 12786177 DOI: 10.1103/physreve.67.051906] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2002] [Indexed: 11/07/2022]
Abstract
Single-molecule experiments on single- and double-stranded DNA have sparked a renewed interest in the force versus extension of polymers. The extensible freely jointed chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA, but this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the discrete persistent chain) that borrows features from both the FJC and the wormlike chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first value for the bend stiffness of the overstretched state. In particular, we find the effective bend stiffness for DNA in this state to be about 12 nm k(B)T, a value quite different from either the B-form or single-stranded DNA.
Collapse
Affiliation(s)
- C Storm
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | |
Collapse
|
42
|
Affiliation(s)
- Arnaud Buhot
- Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, UK
| | - Avraham Halperin
- UMR 5819 (CEA, CNRS, UJF), DRFMC/SI3M, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
| |
Collapse
|
43
|
Debnath P, Cherayil BJ. Conformational properties of randomly flexible heteropolymers. J Chem Phys 2002. [DOI: 10.1063/1.1445748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
44
|
Arteca GA, Tapia O. Protein denaturation in vacuo: Mechanism for centrifugal unfolding of neutral lysozyme. J Chem Phys 2001. [DOI: 10.1063/1.1412865] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
|