1 |
MYLLYHARJU J, KIVIRIKKO K I.. Collagens, modifying enzymes and their mutations in humans, flies and worms. Trends Genet, 2004, 20 (1): 33- 43.
|
2 |
SHOULDERS M D, RAINES R T.. Collagen structure and stability. Annual Review of Biochemistry, 2009, 78, 929- 958.
|
3 |
HEINO J.. The collagen family members as cell adhesion proteins. Bioessays, 2007, 29 (10): 1001- 1010.
|
4 |
BRINCKMANN J. Collagens at a Glance [M]// BRINCKMANN J, NOTBOHM H, MÜLLER P K. Collagen: Primer in Structure, Processing and Assembly. Berlin: Springer, 2005: 1-6.
|
5 |
RAMACHANDRAN G N, SASISEKHARAN V.. Structure of Collagen. Nature, 1961, 190 (4780): 1004- 1005.
|
6 |
RICH A, CRICK F H C.. The molecular structure of collagen. Journal of Molecular Biology, 1961, 3 (5): 483- 506.
|
7 |
MYLLYHARJU J, KIVIRIKKO K I.. Collagens and collagen-related diseases. Annals of Medicine, 2001, 33 (1): 7- 21.
|
8 |
KUIVANIEMI H, TROMP G, PROCKOP D J.. Mutations in fibrillar collagens (types Ⅰ, Ⅱ, Ⅲ, and Ⅹ Ⅰ), fibril-associated collagen (type Ⅰ Ⅹ), and network-forming collagen (type Ⅹ) cause a spectrum of diseases of bone, cartilage, and blood vessels. Human Mutation, 1997, 9 (4): 300- 315.
|
9 |
MARINI J C, FORLINO A, CABRAL W A, et al.. Consortium for osteogenesis imperfecta mutations in the helical domain of type Ⅰ collagen: Regions rich in lethal mutations align with collagen binding sites for integrins and proteoglycans. Human Mutation, 2007, 28 (3): 209- 221.
|
10 |
BECK K, CHAN V C, SHENOY N, et al.. Destabilization of osteogenesis imperfecta collagen-like model peptides correlates with the identity of the residue replacing glycine. Proceedings of the National Academy of Sciences, 2000, 97 (8): 4273- 4278.
|
11 |
BAUM J, BRODSKY B.. Structural biology: Modelling collagen diseases. Nature, 2008, 453 (7198): 998.
|
12 |
BRODSKY B, PERSIKOV A V.. Molecular structure of the collagen triple helix. Advances in Protein Chemistry and Structural Biology, 2005, 70, 301- 339.
|
13 |
FIELDS G B.. A model for interstitial collagen catabolism by mammalian collagenases. Journal of Theoretical Biology, 1991, 153 (4): 585- 602.
|
14 |
OKUYAMA K, HONGO C, FUKUSHIMA R, et al.. Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: implications for proline ring puckering. Biopolymers, 2004, 76 (5): 367- 377.
|
15 |
GOODMAN M, BHUMRALKAR, JEFFERSON E A, et al.. Collagen mimetics. Biopolymers, 1998, 47 (2): 127- 142.
|
16 |
BAUM J, BRODSKY B. Folding of peptide models of collagen and misfolding in disease [J]. Current Opinion in Structural Biology, 1999, 9(1): 122-128.
|
17 |
BELLA J.. A new method for describing the helical conformation of collagen: Dependence of the triple helical twist on amino acid sequence. Journal of Structural Biology, 2010, 170 (2): 377- 391.
|
18 |
OKUYAMA K.. Revisiting the molecular structure of collagen. Connective Tissue Research, 2008, 49 (5): 299- 310.
|
19 |
PERSIKOV A V, RAMSHAW J A, KIRKPATRICK A, et al.. Amino acid propensities for the collagen triple-helix. Biochemistry, 2000, 39 (48): 14960- 14967.
|
20 |
PERSIKOV A V, RAMSHAW J A M, BRODSKY B.. Prediction of collagen stability from amino acid sequence. Journal of Biological Chemistry, 2005, 280 (19): 19343- 19349.
|
21 |
RAMSHAW J A M, SHAH N K, BRODSKY B.. Gly-X-Y tripeptide frequencies in collagen: A context for host–guest triple-helical peptides. Journal of Structural Biology, 1998, 122 (1): 86- 91.
|
22 |
MANJIRI, BHATE, XIN, et al.. Folding and conformational consequences of glycine to alanine replacements at different positions in a collagen model peptide. Biochemistry, 2002, 41 (20): 6539- 6547.
|
23 |
BODIAN D L, MADHAN B, BRODSKY B, et al.. Predicting the clinical lethality of osteogenesis imperfecta from collagen glycine mutations. Biochemistry, 2008, 47 (19): 5424- 5432.
|
24 |
BERG R A, PROCKOP D J.. The thermal transition of a non-hydroxylated form of collagen. Evidence for a role for hydroxyproline in stabilizing the triple-helix of collagen. Biochemical and Biophysical Research Communications, 1973, 52 (1): 115- 120.
|
25 |
BELLA J, EATON M, BRODSKY B, et al.. Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution. Science, 1994, 266 (5182): 75- 81.
|
26 |
LI Y, BRODSKY B, BAUM J.. NMR conformational and dynamic consequences of a gly to ser substitution in an osteogenesis imperfecta collagen model peptide. Journal of Biological Chemistry, 2009, 284 (31): 20660- 20667.
|
27 |
O'LEARY L E R, FALLAS J A, HARTGERINK J D.. Positive and negative design leads to compositional control in AAB collagen heterotrimers. Journal of The American Chemical Society, 2011, 133 (14): 5432- 5443.
|
28 |
XIAO J, SUN X, MADHAN B, et al.. NMR studies demonstrate a unique AAB composition and chain register for a heterotrimeric type Ⅳ collagen model peptide containing a natural interruption site*. Journal of Biological Chemistry, 2015, 290 (40): 24201- 24209.
|
29 |
JALAN A A, HARTGERINK J D.. Simultaneous control of composition and register of an AAB-type collagen heterotrimer. Biomacromolecules, 2013, 14 (1): 179- 185.
|
30 |
XU F, ZAHID S, SILVA T, et al.. Computational design of a collagen A: B: C-type heterotrimer. Journal of the American Chemical Society, 2011, 133 (39): 15260- 15263.
|
31 |
CLEMENTS K A, ACEVEDO-JAKE A M, WALKER D R, et al.. Glycine substitutions in collagen heterotrimers alter triple helical assembly. Biomacromolecules, 2017, 18 (2): 617- 624.
|
32 |
ACEVEDO-JAKE A M, CLEMENTS K A, HARTGERINK J D.. Synthetic, register-specific, AAB heterotrimers to investigate single point Glycine mutations in osteogenesis imperfecta. Biomacromolecules, 2016, 17 (3): 914- 921.
|
33 |
PARK S, KLEIN T E, PANDE V S.. Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations. Biophysical Journal, 2007, 93 (12): 4108- 4115.
|
34 |
MOONEY S D.. Structural models of osteogenesis imperfecta-associated variants in the COL1A1 gene. Molecular & Cellular Proteomics, 2002, 1 (11): 868- 875.
|
35 |
BODIAN D L, RADMER R J, HOLBERT S, et al.. Molecular dynamics simulations of the full triple helical region of collagen type I provide an atomic scale view of the protein's regional heterogeneity. Pacific Symposium on Biocomputing, 2011, 193- 204.
|
36 |
FEI X, ZHENG H, CLAUVELIN N, et al. Parallels between DNA and collagen - Comparing elastic models of the double and triple helix [J]. Scientific Reports, 2017, 7(1): 12802.
|
37 |
ZHENG H, LU C, LAN J, et al.. How electrostatic networks modulate specificity and stability of collagen. Proc Natl Acad Sci USA, 2018, 115 (24): 6207- 6212.
|
38 |
LINDORFF-LARSEN K, PIANA S, PALMO K, et al.. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics, 2010, 78 (8): 1950- 1958.
|
39 |
PRONK S, PÁLL S, SCHULZ R, et al.. GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 2013, 29 (7): 845- 854.
|
40 |
ZHENGWEI P, EWIG C S, HWANG M J, et al.. Comparison of simple potential functions for simulating liquid water. The Journal of Physical Chemistry A, 1997, 101, 7243- 7252.
|
41 |
DARDEN T A, YORK D M, PEDERSEN L G.. Particle mesh Ewald-An N·log(N) method for Ewald sums in large systems. Journal of Computational Chemistry, 1993, 18 (12): 1463- 1472.
|
42 |
BERENDSEN H J C P, POSTMA J P M V, GUNSTEREN W F V, et al.. Molecular-dynamics with coupling to an external bath. The Journal of Chemical Physics, 1984, 81, 3684.
|
43 |
OLSON W K, BANSAL M, BURLEY S K, et al.. A standard reference frame for the description of nucleic acid base-pair geometry. Journal of Molecular Biology, 2001, 313 (1): 229- 237.
|
44 |
OLSON W K.. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences, 1998, 95 (19): 11163- 11168.
|
45 |
LUZAR A, CHANDLER D.. Effect of environment on hydrogen bond dynamics in liquid water. Physrevlett, 1996, 76 (6): 928.
|
46 |
GORDON D B, MARSHALL S A, MAYO S L.. Energy functions for protein design. Current Opinion in Structural Biology, 1999, 9 (4): 509- 513.
|
47 |
FU I, CASE D A, BAUM J.. Dynamic water-mediated hydrogen bonding in a collagen model peptide. Biochemistry, 2015, 54 (39): 6029- 6037.
|
48 |
BABCOCK M S, OLSON W K.. The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters . Journal of Molecular Biology, 1994, 237 (1): 98- 124.
|
49 |
GAJKO-GALICKA A.. Mutations in type Ⅰ collagen genes resulting in osteogenesis imperfecta in humans. Acta Biochimica Polonica, 2002, 49 (2): 433- 441.
|
50 |
KUIVANIEMI H, TROMP G, PROCKOP D J.. Mutations in collagen genes: Causes of rare and some common diseases in humans. Faseb Journal, 1991, 5 (7): 2052- 2060.
|
51 |
WALLACE J M, ERICKSON B, LES C M, et al.. Distribution of type Ⅰ collagen morphologies in bone: Relation to estrogen depletion. Bone, 2010, 46 (5): 1349- 1354.
|
52 |
LI T, CHANG S W, RODRIGUEZ-FLOREZ N, et al.. Studies of chain substitution caused sub-fibril level differences in stiffness and ultrastructure of wildtype and oim/oim collagen fibers using multifrequency-AFM and molecular modeling. Biomaterials, 2016, 107, 15- 22.
|
53 |
XIAO J, MADHAN B, LI Y, et al.. Osteogenesis imperfecta model peptides: Incorporation of residues replacing Gly within a triple helix achieved by renucleation and local flexibility. Biophysical Journal, 2011, 101 (2): 449- 458.
|
54 |
XIAO J, CHENG H, SILVA T, et al.. Osteogenesis imperfecta missense mutations in collagen: Structural consequences of a Glycine to alanine replacement at a highly charged site. Biochemistry, 2011, 50 (50): 10771- 10780.
|