Coarse-Grained Modeling and Simulations of Thermoresponsive …
71
73. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput
Phys 117(1):1–19
74. Hockney RW, Eastwood JW (1988) Computer simulation using particles. CRC Press, Boca
Raton
75. Tuckerman M, Berne BJ, Martyna GJ (1992) Reversible multiple time scale molecular
dynamics. J Chem Phys 97(3):1990–2001
76. Wong K-Y, Pettitt BM (2008) The pathway of oligomeric DNA melting investigated by
molecular dynamics simulations. Biophys J 95(12):5618–5626
77. Sambriski E, Schwartz D, De Pablo J (2009) A mesoscale model of DNA and its renaturation.
Biophys J 96(5):1675–1690
78. Dickerson RE, Drew HR, Conner BN, Wing RM, Fratini AV, Kopka ML (1982) The anatomy
of a-, b-, and z-dna. Science 216(4545):475–485
79. SantaLucia J Jr, Hicks D (2004) The thermodynamics of DNA structural motifs. Annu Rev
Biophys Biomol Struct 33:415–440
80. Blake RD, Bizzaro JW, Blake JD, Day G, Delcourt S, Knowles J, Marx KA, SantaLucia
J Jr (1999) Statistical mechanical simulation of polymeric DNA melting with MELTSIM.
Bioinformatics (Oxford Engl) 15(5):370–375
81. Huguet JM, Bizarro CV, Forns N, Smith SB, Bustamante C, Ritort F (2010) Singlemolecule derivation of salt dependent base-pair free energies in DNA. Proc Natl Acad Sci
107(35):15431–15436
82. Bella J (2016) Collagen structure: new tricks from a very old dog. Biochem J 473(8):1001–
1025
83. Shoulders MD, Raines RT (2009) Collagen structure and stability. Annu Rev Biochem 78:929–
958
84. Bella J, Eaton M, Brodsky B, Berman HM (1994) Crystal and molecular structure of a
collagen-like peptide at 1.9 A resolution. Science 266(5182):75–81
85. Brodsky B, Persikov AV (2005) Molecular structure of the collagen triple helix. Adv Protein
Chem 70:301–339
86. Brodsky B, Ramshaw JA (1997) The collagen triple-helix structure. Matrix Biol 15(8–9):545–
554
87. Sakakibara S, Inouye K, Shudo K, Kishida Y, Kobayashi Y, Prockop DJ (1973) Synthesis of
(Pro-Hyp-Gly) n of defined molecular weights evidence for the stabilization of collagen triple
helix by hydroxypyroline. Biochimica et Biophysica Acta (BBA)-Protein Struct 303(1):198–
202
88. Brown F III, Hopfinger A, Blout E (1972) The collagen-like triple helix to random-chain
transition: experiment and theory. J Mol Biol 63(1):101–115
89. Jin H-E, Jang J, Chung J, Lee HJ, Wang E, Lee S-W, Chung W-J (2015) Biomimetic
self-templated hierarchical structures of collagen-like peptide amphiphiles. Nano Lett
15(10):7138–7145
90. Sarkar B, O’Leary LE, Hartgerink JD (2014) Self-assembly of fiber-forming collagen mimetic
peptides controlled by triple-helical nucleation. J Am Chem Soc 136(41):14417–14424
91. Jalan AA, Jochim KA, Hartgerink JD (2014) Rational design of a non-canonical “stickyended” collagen triple helix. J Am Chem Soc 136(21):7535–7538
92. Jalan AA, Hartgerink JD (2013) Pairwise interactions in collagen and the design of
heterotrimeric helices. Curr Opin Chem Biol 17(6):960–967
93. Luo J, Tong YW (2011) Self-assembly of collagen-mimetic peptide amphiphiles into
biofunctional nanofiber. ACS Nano 5(10):7739–7747
94. Persikov AV, Ramshaw JA, Kirkpatrick A, Brodsky B (2000) Amino acid propensities for the
collagen triple-helix. Biochemistry 39(48):14960–14967
95. Klein TE, Huang CC (1999) Computational investigations of structural changes resulting from
point mutations in a collagen-like peptide. Biopolym Original Res Biomol 49(2):167–183
96. Gautieri A, Vesentini S, Redaelli A, Buehler MJ (2009) Single molecule effects of osteogenesis
imperfecta mutations in tropocollagen protein domains. Protein Sci 18(1):161–168
71
73. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput
Phys 117(1):1–19
74. Hockney RW, Eastwood JW (1988) Computer simulation using particles. CRC Press, Boca
Raton
75. Tuckerman M, Berne BJ, Martyna GJ (1992) Reversible multiple time scale molecular
dynamics. J Chem Phys 97(3):1990–2001
76. Wong K-Y, Pettitt BM (2008) The pathway of oligomeric DNA melting investigated by
molecular dynamics simulations. Biophys J 95(12):5618–5626
77. Sambriski E, Schwartz D, De Pablo J (2009) A mesoscale model of DNA and its renaturation.
Biophys J 96(5):1675–1690
78. Dickerson RE, Drew HR, Conner BN, Wing RM, Fratini AV, Kopka ML (1982) The anatomy
of a-, b-, and z-dna. Science 216(4545):475–485
79. SantaLucia J Jr, Hicks D (2004) The thermodynamics of DNA structural motifs. Annu Rev
Biophys Biomol Struct 33:415–440
80. Blake RD, Bizzaro JW, Blake JD, Day G, Delcourt S, Knowles J, Marx KA, SantaLucia
J Jr (1999) Statistical mechanical simulation of polymeric DNA melting with MELTSIM.
Bioinformatics (Oxford Engl) 15(5):370–375
81. Huguet JM, Bizarro CV, Forns N, Smith SB, Bustamante C, Ritort F (2010) Singlemolecule derivation of salt dependent base-pair free energies in DNA. Proc Natl Acad Sci
107(35):15431–15436
82. Bella J (2016) Collagen structure: new tricks from a very old dog. Biochem J 473(8):1001–
1025
83. Shoulders MD, Raines RT (2009) Collagen structure and stability. Annu Rev Biochem 78:929–
958
84. Bella J, Eaton M, Brodsky B, Berman HM (1994) Crystal and molecular structure of a
collagen-like peptide at 1.9 A resolution. Science 266(5182):75–81
85. Brodsky B, Persikov AV (2005) Molecular structure of the collagen triple helix. Adv Protein
Chem 70:301–339
86. Brodsky B, Ramshaw JA (1997) The collagen triple-helix structure. Matrix Biol 15(8–9):545–
554
87. Sakakibara S, Inouye K, Shudo K, Kishida Y, Kobayashi Y, Prockop DJ (1973) Synthesis of
(Pro-Hyp-Gly) n of defined molecular weights evidence for the stabilization of collagen triple
helix by hydroxypyroline. Biochimica et Biophysica Acta (BBA)-Protein Struct 303(1):198–
202
88. Brown F III, Hopfinger A, Blout E (1972) The collagen-like triple helix to random-chain
transition: experiment and theory. J Mol Biol 63(1):101–115
89. Jin H-E, Jang J, Chung J, Lee HJ, Wang E, Lee S-W, Chung W-J (2015) Biomimetic
self-templated hierarchical structures of collagen-like peptide amphiphiles. Nano Lett
15(10):7138–7145
90. Sarkar B, O’Leary LE, Hartgerink JD (2014) Self-assembly of fiber-forming collagen mimetic
peptides controlled by triple-helical nucleation. J Am Chem Soc 136(41):14417–14424
91. Jalan AA, Jochim KA, Hartgerink JD (2014) Rational design of a non-canonical “stickyended” collagen triple helix. J Am Chem Soc 136(21):7535–7538
92. Jalan AA, Hartgerink JD (2013) Pairwise interactions in collagen and the design of
heterotrimeric helices. Curr Opin Chem Biol 17(6):960–967
93. Luo J, Tong YW (2011) Self-assembly of collagen-mimetic peptide amphiphiles into
biofunctional nanofiber. ACS Nano 5(10):7739–7747
94. Persikov AV, Ramshaw JA, Kirkpatrick A, Brodsky B (2000) Amino acid propensities for the
collagen triple-helix. Biochemistry 39(48):14960–14967
95. Klein TE, Huang CC (1999) Computational investigations of structural changes resulting from
point mutations in a collagen-like peptide. Biopolym Original Res Biomol 49(2):167–183
96. Gautieri A, Vesentini S, Redaelli A, Buehler MJ (2009) Single molecule effects of osteogenesis
imperfecta mutations in tropocollagen protein domains. Protein Sci 18(1):161–168