All issues
- 2024 Vol. 16
- 2023 Vol. 15
- 2022 Vol. 14
- 2021 Vol. 13
- 2020 Vol. 12
- 2019 Vol. 11
- 2018 Vol. 10
- 2017 Vol. 9
- 2016 Vol. 8
- 2015 Vol. 7
- 2014 Vol. 6
- 2013 Vol. 5
- 2012 Vol. 4
- 2011 Vol. 3
- 2010 Vol. 2
- 2009 Vol. 1
Phase transition from α-helices to β-sheets in supercoils of fibrillar proteins
pdf (3492K)
/ Annotation
List of references:
- Моделирование микромеханики биомолекул на графических процессорах с использованием динамики Ланжевена // Мат. Модел. — 2011. — Т. 23, № 10. — С. 133–156. , , и др.
- Elasticity theory of the B-DNA to S-DNA transition // Biophys. J. — 1998. — V. 74. — P. 132–137. — DOI: 10.1016/S0006-3495(98)77774-4. , , .
- Fibrinogen and fibrin as members of the keratin-myosin group // Nature. — 1943. — V. 151, no. 3843. — P. 716–717. — DOI: 10.1038/151716a0. — ads: 1943Natur.151..716B. , , .
- Dynamics of unbinding of cell adhesion molecules: Transition from catch to slip bonds // Proc. Natl. Acad. Sci. USA. — 2005. — V. 102, no. 6. — P. 1835–1839. — DOI: 10.1073/pnas.0406938102. — ads: 2005PNAS..102.1835B. , .
- Models for the specific adhesion of cells to cells // Science. — 1978. — V. 200, no. 4342. — P. 618–627. — DOI: 10.1126/science.347575. — ads: 1978Sci...200..618B. .
- Multiscale Mechanics of Fibrin Polymer: Gel Stretching with Protein Unfolding and Loss of Water // Science. — 2009. — V. 325, no. 5941. — P. 741–744. — DOI: 10.1126/science.1172484. — ads: 2009Sci...325..741B. , , , et al.
- Deformation and failure of protein materials in physiologically extreme conditions and disease // Nat. Mater. — 2009. — V. 8, no. 3. — P. 175–188. — DOI: 10.1038/nmat2387. — ads: 2009NatMa...8..175B. , .
- Entropic elasticity of lambda-phage DNA // Science. — 1994. — V. 265, no. 5178. — P. 1599–1600. — DOI: 10.1126/science.8079175. — ads: 1994Sci...265.1599B. , , , .
- The effects of stretching on wool fibres as monitored by FT-Raman spectroscopy // J. Mol. Struct. — 1998. — V. 440, no. 1-3. — P. 15–23. — DOI: 10.1016/S0022-2860(97)00227-5. — ads: 1998JMoSt.440...15C. , , .
- α-Helical coiled coils and bundles: How to design an α-helical protein // Proteins. — 1990. — V. 7, no. 1. — P. 1–15. — DOI: 10.1002/prot.340070102. , .
- β-Hairpin conformation of fibrillogenic peptides: Structure and α-β transition mechanism revealed by molecular dynamics simulations // Proteins. — 2004. — V. 57, no. 1. — P. 198–204. — DOI: 10.1002/prot.20178. , , , et al.
- Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids // J. Phys. Chem. B. — 1999. — V. 103, no. 18. — P. 3765–3773. — DOI: 10.1021/jp984440c. , .
- The molecular origins of the mechanical properties of fibrin // Biophys. Chem. — 2010. — V. 152, no. 1-3. — P. 15–20. — DOI: 10.1016/j.bpc.2010.08.009. , , .
- Evaluation of a fast implicit solvent model for molecular dynamics simulations // Proteins. — 2002. — V. 46, no. 1. — P. 24–33. — DOI: 10.1002/prot.10001. , , .
- An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution // J. Mol. Biol. — 1996. — V. 256, no. 5. — P. 939–948. — DOI: 10.1006/jmbi.1996.0139. , .
- Knowledge-based protein secondary structure assignment // Proteins. — 1995. — V. 23, no. 4. — P. 566–579. — DOI: 10.1002/prot.340230412. , .
- The Mechanical Properties of Hydrated Intermediate Filaments: Insights from Hagfish Slime Threads // Biophys. J. — 2003. — V. 85, no. 3. — P. 2015–2027. — DOI: 10.1016/S0006-3495(03)74629-3. , , , et al.
- Toward quantification of protein backbone–backbone hydrogen bonding energies: An energetic analysis of an amide-to-ester mutation in an α-helix within a protein // Protein Sci. — 2009. — V. 17, no. 6. — P. 1096–1101. — DOI: 10.1110/ps.083439708. , .
- A Comparison of the Mechanical and Structural Properties of Fibrin Fibers with Other Protein Fibers // Cell Biochem. Biophys. — 2007. — V. 49, no. 3. — P. 165–181. — DOI: 10.1007/s12013-007-9001-4. , , , et al.
- VMD: Visual molecular dynamics // J. Molec. Graphics. — 1996. — V. 14, no. 1. — P. 33–38. — DOI: 10.1016/0263-7855(96)00018-5. , , .
- Steered molecular dynamics and mechanical functions of proteins // Current opinion in structural biology. — 2001. — V. 11, no. 2. — P. 224–30. — DOI: 10.1016/S0959-440X(00)00194-9. , , .
- Crystal Structure of Human Fibrinogen // Biochemistry. — 2009. — V. 48, no. 18. — P. 3877–3886. — DOI: 10.1021/bi802205g. , , , et al.
- New Aspects of the α-Helix to β-Sheet Transition in Stretched Hard α-Keratin Fibers // Biophys. J. — 2004. — V. 87, no. 1. — P. 640–647. — DOI: 10.1529/biophysj.103.036749. , , , .
- Tensile Properties of Single Desmin Intermediate Filaments // Biophys. J. — 2008. — V. 94, no. 7. — P. 2790–2799. — DOI: 10.1529/biophysj.107.119826. , , .
- Molecular Basis of Fibrin Clot Elasticity // Structure. — 2008. — V. 16, no. 3. — P. 449–4596. — DOI: 10.1016/j.str.2007.12.019. , , , .
- The α-helix to β-sheet transition in stretched and compressed hydrated fibrin clots // Biophysical journal. — 2012. — V. 103, no. 5. — P. 1020–7. — DOI: 10.1016/j.bpj.2012.07.046. — ads: 2012BpJ...103.1020L. , , , .
- The mechanical properties of single fibrin fibers // J. Thromb. Haemost. — 2010. — V. 8, no. 5. — P. 1030–1036. , , , .
- All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins // J. Phys. Chem. B. — 1998. — V. 102, no. 18. — P. 3586–3616. — DOI: 10.1021/jp973084f. , , , et al.
- Empirical force fields for biological macromolecules: Overview and issues // J. Comput. Chem. — 2004. — V. 25, no. 13. — P. 1584–1604. — DOI: 10.1002/jcc.20082. .
- Mechanical unfolding intermediates in titin modules // Nature. — 1999. — V. 402, no. 6757. — P. 100–3. — DOI: 10.1038/47083. — ads: 1999Natur.402..100M. , , , et al.
- Recommendations for nomenclature on fibrinogen and fibrin // J. Thromb. Haemost. — 2009. — V. 7, no. 2. — P. 355–359. — DOI: 10.1111/j.1538-7836.2008.03242.x. , .
- Aggregation kinetics of bovine serum albumin studied by FTIR spectroscopy and light scattering // Biophys. Chem. — 2004. — V. 107, no. 2. — P. 175–187. — DOI: 10.1016/j.bpc.2003.09.004. , , , et al.
- Conformational free energy of hydration for the alanine dipeptide: thermodynamic analysis // J. Phys. Chem. — 1988. — V. 92, no. 13. — P. 3994–3997. — DOI: 10.1021/j100324a061. , .
- Protein unfolding accounts for the unusual mechanical behavior of fibrin networks // Acta Biomaterialia. — 2011. — V. 7, no. 6. — P. 2374–2383. — DOI: 10.1016/j.actbio.2011.02.026. , , , et al.
- Molecular Dynamics Simulation of the α-Helix to β-Sheet Transition in Coiled Protein Filaments: Evidence for a Critical Filament Length Scale // Phys. Rev. Lett. — 2010. — V. 104, no. 19. — P. 198304. — DOI: 10.1103/PhysRevLett.104.198304. — ads: 2010PhRvL.104s8304Q. , .
- Hierarchical Structure Controls Nanomechanical Properties of Vimentin Intermediate Filaments // PLoS ONE. — 2009. — V. 10, no. 4. — P. e7294. — ads: 2009PLoSO...4.7294Q. , , .
- Elastically Coupled Two-Level Systems as a Model for Biopolymer Extensibility // Phys. Rev. Lett. — 1998. — V. 81, no. 21. — P. 4764–4767. — DOI: 10.1103/PhysRevLett.81.4764. — ads: 1998PhRvL..81.4764R. , , .
- The myosin coiled-coil is a truly elastic protein structure // Nat. Mater. — 2002. — V. 1, no. 4. — P. 232–235. — DOI: 10.1038/nmat776. — ads: 2002NatMa...1..232S. , , , .
- Protein Structural Perturbation and Aggregation on Homogeneous Surfaces // Biophys. J. — 2005. — V. 88, no. 2. — P. 1322–1333. — DOI: 10.1529/biophysj.104.051797. , .
- Protein unfolding at interfaces: Slow dynamics of α-helix to β-sheet transition // Proteins. — 2004. — V. 56, no. 4. — P. 669–678. — DOI: 10.1002/prot.20183. , , , et al.
- Semianalytical treatment of solvation for molecular mechanics and dynamics // JACS. — 1990. — V. 112, no. 16. — P. 6127–6129. — DOI: 10.1021/ja00172a038. , , , .
- Mutational analysis of designed peptides that undergo structural transition from α helix to β sheet and amyloid fibril formation // Structure. — 2000. — V. 8, no. 9. — P. 915–925. — DOI: 10.1016/S0969-2126(00)00183-0. , , .
- The mechanical properties of fibrin for basic scientists and clinicians // Biophys. Chem. — 2004. — V. 112, no. 2-3. — P. 267–276. — DOI: 10.1016/j.bpc.2004.07.029. — ads: 2004hame.book.....W. .
- Fibrinogen and Fibrin / Fibrous Proteins: Coiled-Coils, Collagen and Elastomers. — Academic Press, 2005. — Parry D. A. D., Squire J. M. (ed.). .
- Fibrinogen and Fibrin // Advances in Protein Chemistry. — 2005. — V. 70. — P. 247–299. — DOI: 10.1016/S0065-3233(05)70008-5. — ads: 1994LNP...432..247W. .
- Mechanism of fibrin(ogen) forced unfolding // Structure. — 2011. — V. 19, no. 11. — P. 1615–1624. — DOI: 10.1016/j.str.2011.08.013. , , , et al.
- SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors // Proteins. — 2010. — V. 78, no. 14. — P. 2984–2999. — DOI: 10.1002/prot.22824. , , , .
- Generation of Random Numbers on Graphics Processors: Forced Indentation In Silico of the Bacteriophage HK97 // J. Phys. Chem. B. — 2011. — V. 115, no. 18. — P. 5278–5288. — DOI: 10.1021/jp109079t. , , , .
Indexed in Scopus
Full-text version of the journal is also available on the web site of the scientific electronic library eLIBRARY.RU
The journal is included in the Russian Science Citation Index
The journal is included in the RSCI
International Interdisciplinary Conference "Mathematics. Computing. Education"
Copyright © 2009–2024 Institute of Computer Science