BSDB - Results of all-atom simulations

Summary of all-atom simulations results on the constant speed stretching of proteins. The symbols are the same as for experimental data. In case of T4 Lysozyme the unfolding force was estimated by the protocol based on the secondary structures of the native state but not by all-atom MD.

Results of constant speed all-atom simulation of stretching of proteins

Protein	PDB	N	F_max [pN]	v_p [Å/ps]	References
Immunoglobulins
I1 oxidized	1gcg	97	2397	0.5	[12]
I1 reduced	1gcg	97	2090	0.5	[12]
I27	1tit	89	2479	1	[2,12]
I27	1tit	89	2040	0.5	[4-7,9]
I28		93	2082	0.5	[4]
I28		93	2554	1	[4]
Fibronectins typeIII
¹FNIII	1oww	97	1500	0.01	[11]
²FNIII	1oww	91	1600	0.01	[11]
⁷FNIII	1fnf	93	1638	0.5	[1,7]
⁹FNIII	1fnf	91	2000	0.1	[1,9,10]
¹⁰FNIII	1fnf	94	1580	0.5	[1,7,9,10]
⁹FNIII	1fnf	91	⁹F<¹⁰F	0.1	[13,14]
Other
ubiquitin (N-C)	1ubq	76	2000	0.1	[3,8]
ubiquitin (48-C)	1ubq	28	1200	0.1	[2,3]
BCA II	1v9c	259	2300	0.5	[16]
barnase	1bnr	108	500	0.01	[15]
7A	1aoh		1360	0.01	[17]
1C	1g1k		1610	0.01	[17]
2A	1anu		860	0.01	[17]
cad1	1edh	211	1850	0.5	[7]
cad2	1edh	211	1970	0.5	[7]
cell adhesion VCAM1	1vsc	89	2050	0.5	[7]
cell adhesion VCAM2	1vsc	108	1620	0.5	[7]
T4 Lysozyme	1b6i	164	75	10⁴	[10]
DDFLN4	1ksr	100	700	0.01	[18]
C-cadherin	1l3w	129	1550	0.01	[19]
ankyrin*4	1n11	132	210	0.01	[19]
cytochrome C6 cc6	1cyi	89	no peak	0.5	[7]
binding protein igb	1bdd	60	no peak	0.5	[7]
synaptotagmin (c2)	1rsy	125	no peak	0.5	[7]

References

[1] Craig, D., Krammer, A., Schulten, K. & Vogel, V. Comparison of the early stages of forced unfolding for fibronectin type III modules. Proc. Natl. Acad. Sci. (USA) 98, 5590-5595 (2001).

[2] Chyan, C-L., Lin, F-C., Peng, H., Yuan, J-M., Chang, C-H., Lin, S-H. & Yang, G. Reversible mechanical unfolding of single ubiquitin molecules. Biophys. J. 87 3995-4006 (2004).

[3] Carrion-Vazquez, M., Li, H., Marszalek, P. E., Obershauser, A. F. & Fernandez, J. M. The mechanical stability of ubiquitin is linkage dependent. Nat. Struc. Biol. 10, 738-743 (2004).

[4] Lu, H., Isralewitz, B., Krammer, A., Vogel, V. & Schulten, K. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 75, 662-671 (1998).

[5] Lu, H. & Schulten, K. Streed molecular dynamics simulations of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observation. Chem.Phys. 247, 141-153 (1999).

[6] Lu, H. & Schulten, K. The key event in force-induced unfolding of titin’s immunoglobulin domains. Biophys. J. 79, 51-65 (2000).

[7] Lu, H. & Schulten, K. Steered Molecular dynamics simulation of force-induced protein domain unfolding. Proteins 35, 453-463 (1999).

[8] Li, P-C. & Makarov, D. E. Simulation of the mechanical unfolding of ubiquitin: Probing different unfolding reaction coordinates by changing the pulling geometry. J. Chem. Phys. 121, 4826-4832 (2004).

[9] Krammer, A., Lu, H., Isralewitz, B., Schulten, K. & Vogel, V. Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. Proc. Natl. Acad. Sci. (USA) 96, 1351-1356 (1999).

[10] Klimov, D. K. & Thirumalai, D. Native topology determines force-induced unfolding pathways in globular proteins. Proc. Natl. Acad. Sci. (USA) 97, 7254- 7259 (2000).

[11] Gao, M., Craig, D., Lequin, O., Campbell, I. D., Vogel, V. & Schulten, K. Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Proc. Natl. Acad. Sci. (USA) 100, 14784-14789 (2003).

[12] Gao, M., Wilmanns, M. & Schulten, K. Steered molecular dynamics studies of titin I1 domain unfolding. Biophys. J. 83, 3435-3445 (2002).

[13] Paci, E. & Karplus, M. Unfolding proteins by external forces and temperature: The importance of topology and energetics. Proc. Natl. Acad. Sci. (USA) 97, 6521-6526 (2000)

[14] Paci, E. & Karplus, M. Forced Unfolding of Fibronectin Type 3 Modules: An Analysis by Biased Molecular Dynamics Simulations. J. Mol. Biol. 288, 441-459 (1999)

[15] Best, R. B., Li, B., Steward, A., Daggett, V. & Clarke, J. Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys. J. 81, 2344-2356 (2001).

[16] S. Ohta, M. T. Alam, H. Arakawa, A. Ikai, Origin of mechanical strength of bovine carbonic anhydrase studied by molecular dynamics simulation. Biophys. J. 87, 4007-4020 (2004).

[17] Valbuena, A., Oroz, J., Hervas, R., Vera, A. M., Rodriguez, D., Menendez, M., Sulkowska, J. I., Cieplak, M. & Carrion-Vazquez, M. On the remarkable mechanostability of scaffoldins and the mechanical clamp motif. Proc. Natl. Acad. Sci. USA 106 13791-13796 (2009).

[18] Kouza, M., Hu, C. K., Zung, H. & Li, M. S. Protein mechanical unfolding: Importance of non-native interactions. J. Chem. Phys. 131 215103-11 (2009).

[19] Sotomayor, M., Corey, D. P. & Schulten, K. In search of the hair-cell gating spring: Elastic properties of ankyrin and cadherin repeats, Structure 13 669-682 (2005).