Chemistry

Theoretical evaluation on thermodynamic stability of chignolin


1.

Dill, Okay. A. Dominant forces in protein folding. Biochemistry 29, 7133–7155 (1990).

2.

Ben-Naim, A. The Rise and Fall of the Hydrophobic Impact in Protein Folding and Protein-Protein Affiliation, and Molecular Recognition. Open Journal of Biophysics 1, 1–7 (2011).

three.

Tempo, C. N., Scholtz, J. M. & Grimsley, G. R. Forces stabilizing proteins. FEBS Lett 588, 2177–2184 (2014).

four.

Mirsky, A. E. & Pauling, L. On the Construction of Native, Denatured, and Coagulated Proteins. Proc. Natl. Acad. Sci. USA 22, 439–447 (1936).

5.

Bernal, J. D. Construction of Proteins. Nature 143, 663–667 (1939).

6.

Pauling, L. & Corey, R. B. Configurations of Polypeptide Chains With Favored Orientations Round Single Bonds: Two New Pleated Sheets. Proc. Natl. Acad. Sci. USA 37, 729–740 (1951).

7.

Pauling, L., Corey, R. B. & Branson, H. R. The construction of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. USA 37, 205–211 (1951).

eight.

Kauzmann, W. Some components within the interpretation of protein denaturation. Adv. Protein Chem. 14, 1–63 (1959).

9.

Jacoesen, C. F. & Linderstrøm-Lang, Okay. Salt Linkages in Proteins. Nature 164, 411–412 (1949).

10.

Chothia, C. Structural invariants in protein folding. Nature 254, 304–308 (1975).

11.

Man, H. R. Amino-Acid Facet-Chain Partition Energies and Distribution of Residues in Soluble-Proteins. Biophys. J. 47, 61–70 (1985).

12.

Tempo, C. N. et al. Contribution of hydrophobic interactions to protein stability. J. Mol. Biol. 408, 514–528 (2011).

13.

Tempo, C. N. Polar Group Burial Contributes Extra to Protein Stability than Nonpolar Group Burial. Biochemistry 40, 310–313 (2001).

14.

Eriksson, A. E. et al. Response of a protein construction to cavity-creating mutations and its relation to the hydrophobic impact. Science 255, 178–183 (1992).

15.

Bunagan, M. R., Gao, J., Kelly, J. W. & Gai, F. Probing the Folding Transition State Construction of the Villin Headpiece Subdomain by way of Facet Chain and Spine Mutagenesis. J. Am. Chem. Soc. 131, 7470–7476 (2009).

16.

Dill, Okay. A. Principle for the Folding and Stability of Globular-Proteins. Biochemistry 24, 1501–1509 (1985).

17.

Yasuda, S., Oshima, H. & Kinoshita, M. Structural stability of proteins in aqueous and nonpolar environments. J Chem Phys 137, 135103–135103 (2012).

18.

Graziano, G. On the molecular origin of chilly denaturation of globular proteins. Phys Chem Chem Phys 12, 14245–14252 (2010).

19.

Sugita, Y. & Okamoto, Y. Duplicate-exchange molecular dynamics methodology for protein folding. Chemical Physics Letters 314, 141–151 (1999).

20.

Itoh, S. G. & Okumura, H. Duplicate-Permutation Technique with the Suwa-Todo Algorithm past the Duplicate-Trade Technique. J. Chem. Principle Comput. 9, 570–581 (2013).

21.

Nakajima, N., Nakamura, H. & Kidera, A. Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides. J Phys Chem B 101, 817–824 (1997).

22.

Paschek, D. & García, A. E. Reversible Temperature and Strain Denaturation of a Protein Fragment: A Duplicate Trade Molecular Dynamics Simulation Examine. Phys. Rev. Lett. 93, 238105 (2004).

23.

Okumura, H. & Okamoto, Y. Multibaric-multithermal ensemble molecular dynamics simulations. J. Comput. Chem. 27, 379–395 (2006).

24.

Paschek, D., Gnanakaran, S. & García, A. E. Simulations of the stress and temperature unfolding of an alpha-helical peptide. Proc. Natl. Acad. Sci. USA 102, 6765–6770 (2005).

25.

Okumura, H. Temperature and stress denaturation of chignolin: Folding and unfolding simulation by multibaric-multithermal molecular dynamics methodology. Proteins 80, 2397–2416 (2012).

26.

Lindorff-Larsen, Okay., Piana, S., Dror, R. O. & Shaw, D. E. How Quick-Folding Proteins Fold. Science 334, 517 (2011).

27.

Piana, S., Lindorff-Larsen, Okay. & Shaw, D. E. Atomic-level description of ubiquitin folding. PNAS 110, 5915–5920 (2013).

28.

Yu, H. A. & Karplus, M. A thermodynamic evaluation of solvation. J Chem Phys 89, 2366–2379 (1988).

29.

Sumi, T., Mitsutake, A. & Maruyama, Y. A solvation-free-energy practical: A reference-modified density practical formulation. J. Comput. Chem. 36, 1359–1369 (2015).

30.

Sumi, T., Mitsutake, A. & Maruyama, Y. Erratum: ‘A solvation‐free‐power practical: A reference‐modified density practical formulation’ [J. Comput. Chem. 2015, 36, 1359–1369]. J. Comput. Chem. 36, 2009–2011 (2015).

31.

Sumi, T., Maruyama, Y., Mitsutake, A. & Koga, Okay. A reference-modified density practical idea: An utility to solvation free-energy calculations for a Lennard-Jones answer. The Journal of Chemical Physics 144, 224104–224104 (2016).

32.

Sumi, T., Maruyama, Y., Mitsutake, A., Mochizuki, Okay. & Koga, Okay. Utility of reference-modified density practical idea: Temperature and stress dependences of solvation free power. J. Comput. Chem. 39, 202–217 (2018).

33.

Honda, S., Yamasaki, Okay., Sawada, Y. & Morii, H. 10 residue folded peptide designed by phase statistics. Construction 12, 1507–1518 (2004).

34.

Calimet, N., Schaefer, M. & Simonson, T. Protein molecular dynamics with the generalized Born/ACE solvent mannequin. Proteins 45, 144–158 (2001).

35.

Khandogin, J. & Brooks, C. L. Towards the correct first-principles prediction of ionization equilibria in proteins. Biochemistry 45, 9363–9373 (2006).

36.

Harris, R. C. & Pettitt, B. M. Analyzing the assumptions underlying continuum-solvent fashions. J. Chem. Principle Comput. 11, 4593–4600 (2015).

37.

Satoh, D., Shimizu, Okay., Nakamura, S. & Terada, T. Folding free-energy panorama of a 10-residue mini-protein, chignolin. FEBS Lett 580, 3422–3426 (2006).

38.

Harada, R. & Kitao, A. Exploring the folding free power panorama of a β-hairpin miniprotein, chignolin, utilizing multiscale free power panorama calculation methodology. J Phys Chem B 115, 8806–8812 (2011).

39.

Kührová, P., De Simone, A., Otyepka, M. & Finest, R. B. Drive-field dependence of chignolin folding and misfolding: comparability with experiment and redesign. Biophys. J. 102, 1897–1906 (2012).

40.

Mitsutake, A. & Takano, H. Leisure mode evaluation and Markov state rest mode evaluation for chignolin in aqueous answer close to a transition temperature. The Journal of Chemical Physics 143, 124111–124111 (2015).

41.

Maruyama, Y. & Mitsutake, A. Evaluation of Structural Stability of Chignolin. J Phys Chem B 122, 3801–3814 (2018).

42.

Kokubo, H., Hu, C. Y. & Pettitt, B. M. Peptide conformational preferences in osmolyte options: switch free energies of decaalanine. J. Am. Chem. Soc. 133, 1849–1858 (2011).

43.

Kokubo, H., Harris, R. C., Asthagiri, D. & Pettitt, B. M. Solvation free energies of alanine peptides: the impact of flexibility. J Phys Chem B 117, 16428–16435 (2013).

44.

Li, L., Bedrov, D. & Smith, G. D. Repulsive solvent-induced interplay between C60 fullerenes in water. Phys. Rev. E 71, 011502 (2005).

45.

Makowski, M., Czaplewski, C., Liwo, A. & Scheraga, H. A. Potential of imply drive of affiliation of enormous hydrophobic particles: towards the nanoscale restrict. J Phys Chem B 114, 993–1003 (2010).

46.

Kuroda, Y., Suenaga, A., Sato, Y., Kosuda, S. & Taiji, M. All-atom molecular dynamics evaluation of multi-peptide programs reproduces peptide solubility in keeping with experimental observations. Sci. Rep. 6, 19479 (2016).

47.

Ben-Naim, A. Inversion of the hydrophobic/hydrophilic paradigm demystifies the protein folding and self-assembly of issues. Worldwide Journal of Physics, https://doi.org/10.12691/ijp (2013).

48.

Durell, S. R. & Ben-Naim, A. Hydrophobic-hydrophilic forces in protein folding. Biopolymers 107 (2017).

49.

Imamura, H. & Kato, M. 3P066 Unfolding of β-hairpin peptides by stress: FT-IR and FRET research (Protein: Property,The 48th Annual Assembly of the Biophysical Society of Japan). Annu Rev Biophys 50, S156 (2010).

50.

Sumi, T. & Sekino, H. Attainable mechanism underlying high-pressure unfolding of proteins: formation of a short-period high-density hydration shell. Phys Chem Chem Phys 13, 15829–15832 (2011).

51.

Chalikian, T. V. & Macgregor, R. B. Origins of pressure-induced protein transitions. J. Mol. Biol. 394, 834–842 (2009).

52.

Salvetti, G., Tombari, E., Mikheeva, L. & Johari, G. P. The Endothermic Results throughout Denaturation of Lysozyme by Temperature Modulated Calorimetry and an Intermediate Response Equilibrium. J Phys Chem B 106, 6081–6087 (2002).

53.

Schön, A., Clarkson, B. R., Jaime, M. & Freire, E. Temperature stability of proteins: Evaluation of irreversible denaturation utilizing isothermal calorimetry. Proteins 85, 2009–2016 (2017).

54.

Makhatadze, G. I. & Privalov, P. L. Energetics of Protein Construction. Advances in Protein Chemistry 47, 307–425 (Elsevier, 1995).

55.

Maritan, A., Micheletti, C., Trovato, A. & Banavar, J. R. Optimum shapes of compact strings. Nature 406, 287–290 (2000).

56.

Hoang, T. X. et al. Widespread attributes of native-state constructions of proteins, disordered proteins, and amyloid. Proc. Natl. Acad. Sci. USA 103, 6883–6888 (2006).

57.

Go, N. & Taketomi, H. Respective Roles of Brief-Vary and Lengthy-Vary Interactions in Protein Folding. Proc. Natl. Acad. Sci. USA 75, 559–563 (1978).

58.

Wu, L., Zhang, J., Qin, M., Liu, F. & Wang, W. Folding of proteins with an all-atom Go-model. J Chem Phys 128, 235103–235103 (2008).

59.

Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling by means of velocity rescaling. J Chem Phys 126, 014101 (2007).

60.

Abraham, M. J. et al. GROMACS: Excessive efficiency molecular simulations by means of multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25 (2015).

61.

Qiu, D., Shenkin, P. S., Hollinger, F. P. & Nonetheless, W. C. The GB/SA Continuum Mannequin for Solvation. A Quick Analytical Technique for the Calculation of Approximate Born Radii. The Journal of Bodily Chemistry A 101, 3005–3014 (1997).

62.

Hornak, V. et al. Comparability of a number of Amber drive fields and growth of improved protein spine parameters. Proteins 65, 712–725 (2006).

63.

Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS – A linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).

64.

Hub, J. S., de Groot, B. L. & van der Spoel, D. g_wham—A Free Weighted Histogram Evaluation Implementation Together with Sturdy Error and Autocorrelation Estimates. J. Chem. Principle Comput. 6, 3713–3720 (2010).


Supply hyperlink
asubhan

wordpress autoblog

amazon autoblog

affiliate autoblog

wordpress web site

web site growth

Show More

Related Articles

Leave a Reply

Your email address will not be published. Required fields are marked *

Close