-
1
-
-
53049092578
-
Theoretical and computational hierarchical nanomechanics of protein materials: Deformation and fracture
-
Buehler MJ, Keten S, Ackbarow T (2008) Theoretical and computational hierarchical nanomechanics of protein materials: Deformation and fracture. Prog Mater Sci, 53:1101-1241.
-
(2008)
Prog Mater Sci
, vol.53
, pp. 1101-1241
-
-
Buehler, M.J.1
Keten, S.2
Ackbarow, T.3
-
2
-
-
53849090669
-
Mechanical engineering of elastomeric proteins: Toward designing new protein building blocks for biomaterials
-
Li H (2008) Mechanical engineering of elastomeric proteins: Toward designing new protein building blocks for biomaterials. Adv Funct Mater, 18:2643-2657.
-
(2008)
Adv Funct Mater
, vol.18
, pp. 2643-2657
-
-
Li, H.1
-
4
-
-
0142011812
-
Cell and molecular mechanics of biological materials
-
Bao G, Suresh S (2003) Cell and molecular mechanics of biological materials. Nat Mater, 2:715-725.
-
(2003)
Nat Mater
, vol.2
, pp. 715-725
-
-
Bao, G.1
Suresh, S.2
-
5
-
-
34249930159
-
Single-molecule experiments in vitro and in silico
-
Sotomayor M, Schulten K (2007) Single-molecule experiments in vitro and in silico. Science, 316:1144-1148.
-
(2007)
Science
, vol.316
, pp. 1144-1148
-
-
Sotomayor, M.1
Schulten, K.2
-
6
-
-
0034533671
-
Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering
-
Carrion-Vazquez M, Oberhauser AF, Fisher TE (2000) Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. Prog Biophys Mol Bio, 74:63-91.
-
(2000)
Prog Biophys Mol Bio
, vol.74
, pp. 63-91
-
-
Carrion-Vazquez, M.1
Oberhauser, A.F.2
Fisher, T.E.3
-
7
-
-
0031848099
-
Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
-
Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K (1998) Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J, 75:662-671.
-
(1998)
Biophys J
, vol.75
, pp. 662-671
-
-
Lu, H.1
Isralewitz, B.2
Krammer, A.3
Vogel, V.4
Schulten, K.5
-
8
-
-
0034612284
-
Unfolding proteins by external forces and temperature: The importance of topology and energetics
-
Paci E, Karplus M (2000) Unfolding proteins by external forces and temperature: The importance of topology and energetics. Proc Natl Acad Sci USA, 97:6521-6526.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 6521-6526
-
-
Paci, E.1
Karplus, M.2
-
9
-
-
0034691149
-
Native topology determines force-induced unfolding pathways in globular proteins
-
Klimov DK, Thirumalai D (2000) Native topology determines force-induced unfolding pathways in globular proteins. Proc Natl Acad Sci USA, 97:7254-7259.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 7254-7259
-
-
Klimov, D.K.1
Thirumalai, D.2
-
10
-
-
0033151955
-
Steered molecular dynamics simulations of force-induced protein domain unfolding
-
Lu H, Schulten K (1999) Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins, 35:453-463.
-
(1999)
Proteins
, vol.35
, pp. 453-463
-
-
Lu, H.1
Schulten, K.2
-
11
-
-
0042508740
-
The mechanical stability of ubiquitin is linkage dependent
-
Carrion-Vazquez M, et al. (2003) The mechanical stability of ubiquitin is linkage dependent. Nat Struct Biol, 10:738-743.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 738-743
-
-
Carrion-Vazquez, M.1
-
12
-
-
33646142064
-
Mechanical resistance of proteins explained using simple molecular models
-
West DK, Brockwell DJ, Olmsted PD, Radford SE, Paci E (2006) Mechanical resistance of proteins explained using simple molecular models. Biophys J, 90:287-297.
-
(2006)
Biophys J
, vol.90
, pp. 287-297
-
-
West, D.K.1
Brockwell, D.J.2
Olmsted, P.D.3
Radford, S.E.4
Paci, E.5
-
13
-
-
0042508741
-
Pulling geometry defines the mechanical resistance of a β-sheet protein
-
Brockwell DJ, et al. (2003) Pulling geometry defines the mechanical resistance of a β-sheet protein. Nat Struct Biol, 10:731-737.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 731-737
-
-
Brockwell, D.J.1
-
14
-
-
0034804341
-
Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation
-
Best RB, Li B, Steward A, Daggett V, Clarke J (2001) Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys J, 81:2344-2356.
-
(2001)
Biophys J
, vol.81
, pp. 2344-2356
-
-
Best, R.B.1
Li, B.2
Steward, A.3
Daggett, V.4
Clarke, J.5
-
15
-
-
23244441268
-
Mechanically unfolding the small, topologically simple protein L
-
Brockwell DJ, Beddard GS, Paci E, West DK (2005) Mechanically unfolding the small, topologically simple protein L. Biophys J, 89:506-519.
-
(2005)
Biophys J
, vol.89
, pp. 506-519
-
-
Brockwell, D.J.1
Beddard, G.S.2
Paci, E.3
West, D.K.4
-
16
-
-
31044449315
-
Nonmechanical protein can have significant mechanical stability
-
Cao Y, Lam C, Wang M, Li H (2006) Nonmechanical protein can have significant mechanical stability. Angew Chem Int Ed Engl, 45:642-645.
-
(2006)
Angew Chem Int Ed Engl
, vol.45
, pp. 642-645
-
-
Cao, Y.1
Lam, C.2
Wang, M.3
Li, H.4
-
17
-
-
33846666463
-
Polyprotein of GB1 is an ideal artificial elastomeric protein
-
Cao Y, Li H (2007) Polyprotein of GB1 is an ideal artificial elastomeric protein. Nat Mater, 6:109-114.
-
(2007)
Nat Mater
, vol.6
, pp. 109-114
-
-
Cao, Y.1
Li, H.2
-
18
-
-
34547151186
-
Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability
-
Sharma D, et al. (2007) Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability. Proc Natl Acad Sci USA, 104:9278-9283.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 9278-9283
-
-
Sharma, D.1
-
19
-
-
43749107950
-
Mechanical biochemistry of proteins one molecule at a time
-
Oberhauser AF, Carrion-Vazquez M (2008) Mechanical biochemistry of proteins one molecule at a time. J Biol Chem, 283:6617-6621.
-
(2008)
J Biol Chem
, vol.283
, pp. 6617-6621
-
-
Oberhauser, A.F.1
Carrion-Vazquez, M.2
-
20
-
-
34547094880
-
Designing an extracellular matrix protein with enhanced mechanical stability
-
Ng SP, et al. (2007) Designing an extracellular matrix protein with enhanced mechanical stability. Proc Natl Acad Sci USA, 104:9633-9637.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 9633-9637
-
-
Ng, S.P.1
-
21
-
-
52449107719
-
An effective strategy for the design of proteins with enhanced mechanical stability
-
Borgia A, Steward A, Clarke J (2008) An effective strategy for the design of proteins with enhanced mechanical stability. Angew Chem Int Ed Engl, 47:6900-6903.
-
(2008)
Angew Chem Int Ed Engl
, vol.47
, pp. 6900-6903
-
-
Borgia, A.1
Steward, A.2
Clarke, J.3
-
22
-
-
49649083370
-
Single molecule force spectroscopy reveals engineered metal chelation is a general approach to enhance mechanical stability of proteins
-
Cao Y, Yoo T, Li H (2008) Single molecule force spectroscopy reveals engineered metal chelation is a general approach to enhance mechanical stability of proteins. Proc Natl Acad Sci USA, 105:11152-11157.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 11152-11157
-
-
Cao, Y.1
Yoo, T.2
Li, H.3
-
23
-
-
0031011695
-
Reversible unfolding of individual titin immunoglobulin domains by AFM
-
Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science, 276:1109-1112.
-
(1997)
Science
, vol.276
, pp. 1109-1112
-
-
Rief, M.1
Gautel, M.2
Oesterhelt, F.3
Fernandez, J.M.4
Gaub, H.E.5
-
24
-
-
0033523904
-
Mechanical unfolding intermediates in titin modules
-
Marszalek PE, et al. (1999) Mechanical unfolding intermediates in titin modules. Nature, 402:100-103.
-
(1999)
Nature
, vol.402
, pp. 100-103
-
-
Marszalek, P.E.1
-
25
-
-
0033917135
-
The key event in force-induced unfolding of titin's immunoglobulin domains
-
Lu H, Schulten K (2000) The key event in force-induced unfolding of titin's immunoglobulin domains. Biophys J, 79:51-65.
-
(2000)
Biophys J
, vol.79
, pp. 51-65
-
-
Lu, H.1
Schulten, K.2
-
26
-
-
0033616713
-
Mechanical and chemical unfolding of a single protein: A comparison
-
Carrion-Vazquez M, et al. (1999) Mechanical and chemical unfolding of a single protein: A comparison. Proc Natl Acad Sci USA, 96:3694-3699.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3694-3699
-
-
Carrion-Vazquez, M.1
-
27
-
-
33748046806
-
Anisotropic deformation response of single protein molecules
-
Dietz H, Berkemeier F, Bertz M, Rief M (2006) Anisotropic deformation response of single protein molecules. Proc Natl Acad Sci USA, 103:12724-12728.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 12724-12728
-
-
Dietz, H.1
Berkemeier, F.2
Bertz, M.3
Rief, M.4
-
28
-
-
1642493664
-
Tuning the mechanical stability of fibronectin type III modules through sequence variations
-
Craig D, Gao M, Schulten K, Vogel V (2004) Tuning the mechanical stability of fibronectin type III modules through sequence variations. Structure, 12:21-30.
-
(2004)
Structure
, vol.12
, pp. 21-30
-
-
Craig, D.1
Gao, M.2
Schulten, K.3
Vogel, V.4
-
29
-
-
34547635651
-
Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability
-
Sykes MT, Levitt M (2007) Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability. Proc Natl Acad Sci USA, 104:12336-12340.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 12336-12340
-
-
Sykes, M.T.1
Levitt, M.2
-
30
-
-
0038047136
-
The crystal structure of Af1521 a protein from Archaeoglobus fulgidus with homology to the non-histone domain of MacroH2A
-
Allen MD, Buckle AM, Cordell SC, Löwe J, Bycroft M (2003) The crystal structure of Af1521 a protein from Archaeoglobus fulgidus with homology to the non-histone domain of MacroH2A. J Mol Biol, 330:503-511.
-
(2003)
J Mol Biol
, vol.330
, pp. 503-511
-
-
Allen, M.D.1
Buckle, A.M.2
Cordell, S.C.3
Löwe, J.4
Bycroft, M.5
-
31
-
-
21244444665
-
The macro domain is an ADP-ribose binding module
-
Karras GI, et al. (2005) The macro domain is an ADP-ribose binding module. EMBO J, 24:1911-1920.
-
(2005)
EMBO J
, vol.24
, pp. 1911-1920
-
-
Karras, G.I.1
-
32
-
-
63149116496
-
Combining affinity purification by ADP-ribose-binding macro domains with mass spectrometry to define the mammalian ADP-ribosyl proteome
-
Dani N, et al. (2009) Combining affinity purification by ADP-ribose-binding macro domains with mass spectrometry to define the mammalian ADP-ribosyl proteome. Proc Natl Acad Sci USA, 106:4243-4248.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 4243-4248
-
-
Dani, N.1
-
33
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
KabschW, Sander C (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
34
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
Zhang Y, Skolnick J (2005) TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Res, 33:2302-2309.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
35
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang Y, Skolnick J (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57:702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
36
-
-
0344736695
-
Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates
-
Gao M, et al. (2003) Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Proc Natl Acad Sci USA, 100:14784-14789.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 14784-14789
-
-
Gao, M.1
-
37
-
-
10044247452
-
Mechanical unfolding intermediates observed by single-molecule force spectroscopy in a fibronectin type III module
-
Li L, Huang HH, Badilla CL, Fernandez JM (2005) Mechanical unfolding intermediates observed by single-molecule force spectroscopy in a fibronectin type III module. J Mol Biol, 345:817-826.
-
(2005)
J Mol Biol
, vol.345
, pp. 817-826
-
-
Li, L.1
Huang, H.H.2
Badilla, C.L.3
Fernandez, J.M.4
-
38
-
-
42149186359
-
Solvent molecules bridge the mechanical unfolding transition state of a protein
-
Dougan L, Feng G, Lu H, Fernandez JM (2008) Solvent molecules bridge the mechanical unfolding transition state of a protein. Proc Natl Acad Sci USA, 105:3185-3190.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 3185-3190
-
-
Dougan, L.1
Feng, G.2
Lu, H.3
Fernandez, J.M.4
-
39
-
-
33745714406
-
Mechanism of titin unfolding by force: Insight from quasi-equilibrium molecular dynamics calculations
-
Pabon G, Amzel LM (2006) Mechanism of titin unfolding by force: Insight from quasi-equilibrium molecular dynamics calculations. Biophys J, 91:467-472.
-
(2006)
Biophys J
, vol.91
, pp. 467-472
-
-
Pabon, G.1
Amzel, L.M.2
-
40
-
-
33748028865
-
Cysteine engineering of polyproteins for single-molecule force spectroscopy
-
Dietz H, et al. (2006) Cysteine engineering of polyproteins for single-molecule force spectroscopy. Nat Protoc, 1:80-84.
-
(2006)
Nat Protoc
, vol.1
, pp. 80-84
-
-
Dietz, H.1
-
42
-
-
33845979460
-
Contour length and refolding rate of a small protein controlled by engineered disulfide bonds
-
Ainavarapu SRK, et al. (2007) Contour length and refolding rate of a small protein controlled by engineered disulfide bonds. Biophys J, 92:225-233.
-
(2007)
Biophys J
, vol.92
, pp. 225-233
-
-
Ainavarapu, S.R.K.1
-
43
-
-
41149180083
-
Atomic force microscopy reveals parallel mechanical unfolding pathways of T4 lysozyme: Evidence for a kinetic partitioning mechanism
-
Peng Q, Li H (2008) Atomic force microscopy reveals parallel mechanical unfolding pathways of T4 lysozyme: Evidence for a kinetic partitioning mechanism. Proc Natl Acad Sci USA, 105:1885-1890.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 1885-1890
-
-
Peng, Q.1
Li, H.2
-
44
-
-
0018101150
-
Models for specific adhesion of cells to cells
-
Bell GI (1978) Models for specific adhesion of cells to cells. Science, 200:618-627.
-
(1978)
Science
, vol.200
, pp. 618-627
-
-
Bell, G.I.1
-
45
-
-
0031001349
-
Dynamic strength of molecular adhesion bonds
-
Evans E, Ritchie K (1997) Dynamic strength of molecular adhesion bonds. Biophys J, 72:1541-1555.
-
(1997)
Biophys J
, vol.72
, pp. 1541-1555
-
-
Evans, E.1
Ritchie, K.2
-
46
-
-
35348959904
-
Secondary structure, mechanical stability, and location of transition state of proteins
-
Li MS (2007) Secondary structure, mechanical stability, and location of transition state of proteins. Biophys J, 93:2644-2654.
-
(2007)
Biophys J
, vol.93
, pp. 2644-2654
-
-
Li, M.S.1
-
47
-
-
56049108131
-
Stabilization provided by neighboring strands is critical for the mechanical stability of proteins
-
Sharma D, et al. (2008) Stabilization provided by neighboring strands is critical for the mechanical stability of proteins. Biophys J, 95:3935-3942.
-
(2008)
Biophys J
, vol.95
, pp. 3935-3942
-
-
Sharma, D.1
-
49
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B, 102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
-
50
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem, 26:1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
|