肽的折叠热力学
Folding thermodynamics of peptides.
作者信息
Irbäck Anders, Mohanty Sandipan
机构信息
Complex Systems Division, Department of Theoretical Physics, Lund University, Lund, Sweden.
出版信息
Biophys J. 2005 Mar;88(3):1560-9. doi: 10.1529/biophysj.104.050427. Epub 2004 Dec 21.
Abstract
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with approximately 20 residues each. The test set contains both alpha-helical (Trp cage, F(s)) and beta-sheet (GB1p, GB1m2, GB1m3, Betanova, LLM) peptides. The model, which is entirely sequence-based, is able to fold these different peptides for one and the same choice of model parameters. Furthermore, the melting behavior of the peptides is in good quantitative agreement with experimental data. Apparent folded populations obtained using different observables are compared, and are found to be very different for some of the peptides (e.g., Betanova). In other cases (in particular, GB1m2 and GB1m3), the different estimates agree reasonably well, indicating a more two-state-like melting behavior.
摘要
讨论了一种用于原子水平蛋白质折叠研究的简化相互作用势，并在一组每条约有20个残基的肽上进行了测试。测试集包含α-螺旋（色氨酸笼，F(s)）和β-折叠（GB1p、GB1m2、GB1m3、Betanova、LLM）肽。该模型完全基于序列，对于相同的模型参数选择，能够折叠这些不同的肽。此外，肽的解链行为与实验数据在定量上吻合良好。比较了使用不同可观测量获得的表观折叠群体，发现对于某些肽（例如，Betanova）差异很大。在其他情况下（特别是GB1m2和GB1m3），不同的估计结果相当吻合，表明解链行为更类似两态。
相似文献
1
Folding thermodynamics of peptides.肽的折叠热力学
Biophys J. 2005 Mar;88(3):1560-9. doi: 10.1529/biophysj.104.050427. Epub 2004 Dec 21.
2
The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage.色氨酸笼全原子Go模型的平衡性质和折叠动力学。
J Chem Phys. 2005 Mar 15;122(11):114901. doi: 10.1063/1.1874812.
3
Phase diagram of alpha-helical and beta-sheet forming peptides.α-螺旋和β-折叠构象肽的相图。
Phys Rev Lett. 2010 Apr 23;104(16):168105. doi: 10.1103/PhysRevLett.104.168105.
4
Folding thermodynamics of three beta-sheet peptides: a model study.三种β-折叠肽的折叠热力学：一项模型研究。
Proteins. 2004 Jul 1;56(1):110-6. doi: 10.1002/prot.20157.
5
PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides.用于蛋白质模拟的PACE力场。2. 肽的折叠模拟。
J Chem Theory Comput. 2010 Nov 9;6(11):3390-402. doi: 10.1021/ct100313a.
6
Peptide folding in the presence of interacting protein crowders.在存在相互作用的蛋白质拥挤剂的情况下肽的折叠。
J Chem Phys. 2016 May 7;144(17):175105. doi: 10.1063/1.4948462.
7
Molecular dynamics simulation of folding of a short helical peptide with many charged residues.具有多个带电残基的短螺旋肽折叠的分子动力学模拟
J Phys Chem B. 2005 Oct 27;109(42):19980-6. doi: 10.1021/jp052349k.
8
Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins.理解折叠与设计：“色氨酸笼”微型蛋白质的副本交换模拟
Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7587-92. doi: 10.1073/pnas.1330954100. Epub 2003 Jun 13.
9
Design and NMR conformational study of a beta-sheet peptide based on Betanova and WW domains.基于Betanova和WW结构域的β-折叠肽的设计与核磁共振构象研究
Protein Sci. 2006 Oct;15(10):2278-89. doi: 10.1110/ps.062186506. Epub 2006 Sep 8.
10
Structure change of β-hairpin induced by turn optimization: an enhanced sampling molecular dynamics simulation study.β-发夹结构由转角优化引起的变化：增强采样分子动力学模拟研究。
J Chem Phys. 2011 Dec 21;135(23):235104. doi: 10.1063/1.3668288.
引用本文的文献
1
When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina.当外来基因遇到其同源物时：对羊茅属植物两个 PgiC 基因座的计算生物物理分析。
Sci Rep. 2020 Oct 30;10(1):18752. doi: 10.1038/s41598-020-75650-0.
2
Sampling of the conformational landscape of small proteins with Monte Carlo methods.用蒙特卡罗方法对小蛋白构象进行采样。
Sci Rep. 2020 Oct 23;10(1):18211. doi: 10.1038/s41598-020-75239-7.
3
Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy.通过二维红外光谱对色氨酸笼疏水核心动态结构进行无扰检测。
J Phys Chem Lett. 2020 Feb 6;11(3):832-837. doi: 10.1021/acs.jpclett.9b03706. Epub 2020 Jan 21.
4
Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments.通过将模拟与单分子实验进行比较来探究α-突触核蛋白聚集的基础。
Biophys J. 2019 Sep 17;117(6):1125-1135. doi: 10.1016/j.bpj.2019.08.013. Epub 2019 Aug 16.
5
A Monte Carlo Study of the Early Steps of Functional Amyloid Formation.功能性淀粉样蛋白形成早期步骤的蒙特卡罗研究
PLoS One. 2016 Jan 8;11(1):e0146096. doi: 10.1371/journal.pone.0146096. eCollection 2016.
6
Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.用于匹配显式溶剂模拟数据的全原子隐式溶剂力场的变分优化
J Chem Theory Comput. 2013 Dec 10;9(12):5641-5652. doi: 10.1021/ct400730n.
7
Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage.利用D-氨基酸阐明蛋白质折叠机制：应用于色氨酸笼。
Chem Phys. 2013 Aug 30;422. doi: 10.1016/j.chemphys.2013.01.021.
8
PRIMO: A Transferable Coarse-grained Force Field for Proteins.PRIMO：一种适用于蛋白质的可转移粗粒度力场。
J Chem Theory Comput. 2013 Aug 13;9(8):3769-3788. doi: 10.1021/ct400230y.
9
Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains.用于折叠模拟的混合联合原子与粗粒度力场的进一步优化：改进的主链水合作用及带电侧链间的相互作用
J Chem Theory Comput. 2012 Nov 13;8(11):4413-4424. doi: 10.1021/ct300696c. Epub 2012 Oct 11.
10
Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization.离散分子动力学：精细蛋白质特性描述的高效通用模拟方法。
J Phys Chem B. 2012 Jul 26;116(29):8375-82. doi: 10.1021/jp2114576. Epub 2012 Feb 10.
本文引用的文献
1
Oligomerization of amyloid Abeta16-22 peptides using hydrogen bonds and hydrophobicity forces.使用氢键和疏水力使淀粉样β-蛋白16-22肽寡聚化。
Biophys J. 2004 Dec;87(6):3657-64. doi: 10.1529/biophysj.104.046839. Epub 2004 Sep 17.
2
Folding of small proteins using a single continuous potential.利用单一连续势对小蛋白质进行折叠。
J Chem Phys. 2004 May 1;120(17):8271-6. doi: 10.1063/1.1689643.
3
Complex folding pathways in a simple beta-hairpin.简单β-发夹中的复杂折叠途径
Proteins. 2004 Aug 15;56(3):464-74. doi: 10.1002/prot.20127.
4
Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin.通过环设计增强发夹稳定性：以蛋白质G B1结构域发夹为例
J Am Chem Soc. 2004 Jun 16;126(23):7238-43. doi: 10.1021/ja0379520.
5
Folding thermodynamics of three beta-sheet peptides: a model study.三种β-折叠肽的折叠热力学：一项模型研究。
Proteins. 2004 Jul 1;56(1):110-6. doi: 10.1002/prot.20157.
6
Protein folding and misfolding.蛋白质折叠与错误折叠。
Nature. 2003 Dec 18;426(6968):884-90. doi: 10.1038/nature02261.
7
Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent.α-螺旋肽折叠平衡的模拟：广义玻恩近似与显式溶剂的比较。
Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):13934-9. doi: 10.1073/pnas.2232868100. Epub 2003 Nov 14.
8
Reproducible protein folding with the stochastic tunneling method.用随机隧穿方法实现可重复的蛋白质折叠。
Phys Rev Lett. 2003 Oct 10;91(15):158102. doi: 10.1103/PhysRevLett.91.158102. Epub 2003 Oct 6.
9
Trp-cage: folding free energy landscape in explicit water.色氨酸笼：在纯水中的折叠自由能景观
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13280-5. doi: 10.1073/pnas.2233312100. Epub 2003 Oct 27.
10
Transition-path sampling of beta-hairpin folding.β-发夹折叠的过渡路径采样
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12129-34. doi: 10.1073/pnas.1534924100. Epub 2003 Oct 1.
Zotero 插件