Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method
Tóm tắt
Từ khóa
Tài liệu tham khảo
Atilgan AR et al (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80(1):505–515
Balzer EM, Konstantopoulos K (2012) Intercellular adhesion: mechanisms for growth and metastasis of epithelial cancers. Wiley Interdiscip Rev Syst Biol Med 4(2):171–181
Barsegov V, Thirumalai D (2006) Dynamic competition between catch and slip bonds in selectins bound to ligands. J Phys Chem B 110(51):26403–26412
Boggon TJ et al (2002) C-cadherin ectodomain structure and implications for cell adhesion mechanisms. Science 296(5571):1308–1313
Burridge K, Connell L (1983) A new protein of adhesion plaques and ruffling membranes. J Cell Biol 97(2):359–367
Cailliez F, Lavery R (2005) Cadherin mechanics and complexation: the importance of calcium binding. Biophys J 89(6):3895–3903
Cairo CW (2007) Signaling by committee: receptor clusters determine pathways of cellular activation. ACS Chem Biol 2(10):652–655
Care BR, Soula HA (2013) Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime. Phys Rev E 87(1):012720
Chen J, Zolkiewska A (2011) Force-induced unfolding simulations of the human Notch1 negative regulatory region: possible roles of the heterodimerization domain in mechanosensing. PLoS One 6(7):e22837
Cieplak M, Hoang TX, Robbins MO (2002) Folding and stretching in a Go-like model of titin. Proteins 49(1):114–124
Cieplak M, Hoang TX, Robbins MO (2004) Thermal effects in stretching of Go-like models of titin and secondary structures. Proteins 56(2):285–297
Clementi C, Nymeyer H, Onuchic JN (2000) Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 298(5): 937–953
DuFort CC, Paszek MJ, Weaver VM (2011) Balancing forces: architectural control of mechanotransduction. Nat Rev Mol Cell Biol 12(5):308–319
Fooksman DR et al (2010) Functional anatomy of T cell activation and synapse formation. Annu Rev Immunol 28:79–105
Genchev GZ et al (2009) Mechanical signaling on the single protein level studied using steered molecular dynamics. Cell Biochem Biophys 55(3):141–152
Ha T et al (1999) Ligand-induced conformational changes observed in single RNA molecules. Proc Natl Acad Sci USA 96(16):9077–9082
Hardin C, Luthey-Schulten Z, Wolynes PG (1999) Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides. Proteins 34(3):281–294
Hartman NC, Groves JT (2011) Signaling clusters in the cell membrane. Curr Opin Cell Biol 23(4):370–376
Hills RD Jr, Brooks CL III (2009) Insights from coarse-grained Go models for protein folding and dynamics. Int J Mol Sci 10(3):889–905
Hsin J, Schulten K (2011) Improved resolution of tertiary structure elasticity in muscle protein. Biophys J 100(4):L22–L24
Hyeon C, Thirumalai D (2005) Mechanical unfolding of RNA hairpins. Proc Natl Acad Sci USA 102(19):6789–6794
Hyeon C, Thirumalai D (2007) Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J 92(3):731–743
Hytonen VP, Vogel V (2008) How force might activate talin’s vinculin binding sites: SMD reveals a structural mechanism. PLoS Comput Biol 4(2):e24
Improta S, Politou AS, Pastore A (1996) Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure 4(3):323–337
Ingber DE (2006) Cellular mechanotransduction: putting all the pieces together again. FASEB J 20(7):811–827
Isralewitz B, Gao M, Schulten K (2001) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11(2):224–230
Janmey PA, McCulloch CA (2007) Cell mechanics: integrating cell responses to mechanical stimuli. Annu Rev Biomed Eng 9:1–34
Jeffrey GA (1997) An introduction to hydrogen bonding. Oxford University Press, Oxford
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12):2577–2637
Kalyaanamoorthy S, Chen YP (2014) A steered molecular dynamics mediated hit discovery for histone deacetylases. Phys Chem Chem Phys 16(8):3777–3791
Karanicolas J, Brooks CL III (2002) The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci 11(10):2351–2361
Karanicolas J, Brooks CL III (2003) Improved Go-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions. J Mol Biol 334(2):309–325
Klimov DK, Betancourt MR, Thirumalai D (1998) Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. Fold Des 3(6):481–496
Knott M, Best RB (2012) A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations. PLoS Comput Biol 8(7):e1002605
Koga N, Takada S (2001) Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. J Mol Biol 313(1):171–180
Kostetskii I et al (2001) Differential adhesion leads to segregation and exclusion of N-cadherin-deficient cells in chimeric embryos. Dev Biol 234(1):72–79
Labrador V et al (2003) Interactions of mechanotransduction pathways. Biorheology 40(1–3):47–52
Li GH, Cui Q (2002) A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca $$^{2+}$$ 2 + -ATPase. Biophys J 83(5):2457–2474
Liu B et al (2014) Accumulation of dynamic catch bonds between TCR and agonist peptide-MHC triggers T cell signaling. Cell 157(2):357–368
Liu B et al (2014) 2D TCR-pMHC-CD8 kinetics determines T-cell responses in a self-antigen-specific TCR system. Eur J Immunol 44(1):239–250
Lu H et al (1998) Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J 75(2):662–671
Ma J (2004) New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr Protein Pept Sci 5(2):119–123
Ma J (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13(3):373–380
Manibog K et al (2014) Resolving the molecular mechanism of cadherin catch bond formation. Nat Commun 5:3941
Marshall KC (1994) Microbial adhesion in biotechnological processes. Curr Opin Biotechnol 5(3):296–301
Martin HS, Jha S, Coveney PV (2014) Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force. J Comput Chem 35(9):692–702
Martino MM et al (2009) Controlling integrin specificity and stem cell differentiation in 2D and 3D environments through regulation of fibronectin domain stability. Biomaterials 30(6):1089–1097
Merkel R et al (1999) Energy landscapes of receptor–ligand bonds explored with dynamic force spectroscopy. Nature 397(6714):50–53
Patel JS et al (2014) Steered molecular dynamics simulations for studying protein–ligand interaction in cyclin-dependent kinase 5. J Chem Inf Model 54(2):470–480
Pereverzev YV et al (2005) The two-pathway model for the catch–slip transition in biological adhesion. Biophys J 89(3):1446–1454
Ravikumar KM, Huang W, Yang S (2012) Coarse-grained simulations of protein–protein association: an energy landscape perspective. Biophys J 103(4):837–845
Rico F et al (2013) High-speed force spectroscopy unfolds titin at the velocity of molecular dynamics simulations. Science 342(6159):741–743
Rief M et al (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276(5315): 1109–1112
Schwartz MA (2009) Sci Cell Biol. The force is with us 323(5914): 588–589
Schwartz MA, DeSimone DW (2008) Cell adhesion receptors in mechanotransduction. Curr Opin Cell Biol 20(5):551–556
Sotomayor M, Corey DP, Schulten K (2005) In search of the hair-cell gating spring elastic properties of ankyrin and cadherin repeats. Structure 13(4):669–682
Sotomayor M et al (2010) Structural determinants of cadherin-23 function in hearing and deafness. Neuron 66(1):85–100
Sotomayor M, Schulten K (2008) The allosteric role of the Ca $$^{2+}$$ 2 + switch in adhesion and elasticity of C-cadherin. Biophys J 94(12): 4621–4633
Sotomayor M, Schulten K (2008) The allosteric role of the Ca $$^{2+}$$ 2 + switch in adhesion and elasticity of C-cadherin. Biophys J 94(12): 4621–4633
Svoboda K, Block SM (1994) Biological applications of optical forces. Annu Rev Biophys Biomol Struct 23:247–285
Wagner UG et al (1995) Structure determination of the biliverdin apomyoglobin complex: crystal structure analysis of two crystal forms at 1.4 and 1.5 Å resolution. J Mol Biol 247(2):326–337
Willemsen OH et al (2000) Biomolecular interactions measured by atomic force microscopy. Biophys J 79(6):3267–3281
Wlodawer A, Borkakoti N, Moss DS, Howlin B (1986) Comparison of two independently refined models of ribonuclease-A. Acta Cryst B42:379–387
Wu S, Skolnick J, Zhang Y (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 5:17
Wu YH et al (2011) Transforming binding affinities from three dimensions to two with application to cadherin clustering. Nature 475(7357):510–513
Yang S, Roux B (2008) Src kinase conformational activation: thermodynamics, pathways, and mechanisms. PLoS Comput Biol 4(3):e1000047
Yao M et al (2014) Mechanical activation of vinculin binding to talin locks talin in an unfolded conformation. Sci Rep 4:4610
Yokosuka T, Saito T (2010) The immunological synapse, TCR microclusters, and T cell activation. In: Saito T, Batista FD (eds) Immunological synapse. Springer, Berlin, pp 81–107
Zhang C et al (2004) An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 13(2):400–411
Zheng W et al (2012) Predictive energy landscapes for protein–protein association. Proc Natl Acad Sci USA 109(47):19244–19249
Zheng W (2014) All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex. Proteins 82(7): 1376–1386