Coarse-Grained Modeling and Simulations of Thermoresponsive …
51
CLP strand adopts a left-handed polyproline II type (PPII) helix conformation and
three CLP strands come together through inter-strand h-bonding to form a righthanded collagen triple helix [82, 83]. Specifically, the CLP triple helix is stabilized by
inter-strand h-bonds involving the N–H hydrogen of glycine and the C = O oxygen of
proline. Furthermore, the CLP triple helix is thermoresponsive and as the temperature
is increased these inter-chain h-bonds melt and the CLP triple helix dissociates into
individual strands. The melting temperature, T m , of the CLP triple helix is a function
of the number of (X–Y-G) repeat units in each CLP strand [87], the identity of the
amino acids located at the X and Y positions [82, 86], and solvent quality [88]. As a
result, CLPs have been used in several biomedical applications such as drug delivery
and tissue engineering due to their thermal stability, biocompatibility, and ability to
recapitulate the mechanical and chemical properties of the ECM [89–93].
There have been a significant number of studies aimed at relating the composition of CLPs to the triple helix stability and melting temperature. For example, it
is accepted that CLPs containing hydroxyproline, O, have higher melting temperatures than CLPs which lack hydroxyproline. Persikov et al. used a host–guest peptide
system to investigate the amino acid propensities for the collagen triple helix [94].
Using circular dichroism spectroscopy, they showed that the most stable residues
in the Y position of (X–Y-G) amino acid triplets are Hyp and Arg while the most
stabilizing residue in the X position is Pro. Short collagen-like sequences comprising
fewer than ten (X–Y-G) amino acid triplets have also been crystallized and characterized via experimental and computational approaches [84, 95–97]. All-atom MD
simulations of (POG) 4 (POA)(POG) 4 by Klein and Huang showed that waters occupying the water bridge h-bonds were not tightly bound, which led them to assert that
collagen’s extra stability does not arise from h-bonding mediated by a network of
bridging waters [95]. Other studies have also shown that hydroxyproline’s stabilizing
effect has been attributed to stereoelectronic effects rather than its ability to partake
in water-mediated h-bonding. These stereoelectronic effects involve gauche and n
→ π * interactions which pre-organize the collagen backbone such that each peptide
chain adopts the correct backbone dihedral angles for the PPII helix conformation
[82, 83]. Other computational studies have also focused on the mechanical properties
of CLPs such as their elastic moduli. Gautieri et al. conducted atomistic MD simulations of CLPs containing glycine mutations and showed that these mutated peptides
display softer mechanical properties than wild-type tropocollagen molecules [96,
97]. These results have important implications for diseases such as Osteogenesis
Imperfecta where glycine mutations in type I collagen genes can lead to a loss of
structural integrity of the body’s tissues and in some cases, even prenatal death.
Besides the above studies describing the effect of hydroxyproline and glycine
mutations on the thermal and mechanical stability of CLP triple helices, there have
also been several computational studies focused on the effects of sequence length
[98], amino acid substitutions [99] and amino acid stereochemistry [100] (i.e., L
versus D isomers) specifically on the thermal stability of the CLP triple helix. Raman
et al. performed all-atom MD simulations of two host–guest peptides designed by
replacing aspartic acid in the X and Y positions of (GPO)-based CLPs [99]. They
showed that aspartic acid when located at the Y position (i.e., GPD) destabilizes the
51
CLP strand adopts a left-handed polyproline II type (PPII) helix conformation and
three CLP strands come together through inter-strand h-bonding to form a righthanded collagen triple helix [82, 83]. Specifically, the CLP triple helix is stabilized by
inter-strand h-bonds involving the N–H hydrogen of glycine and the C = O oxygen of
proline. Furthermore, the CLP triple helix is thermoresponsive and as the temperature
is increased these inter-chain h-bonds melt and the CLP triple helix dissociates into
individual strands. The melting temperature, T m , of the CLP triple helix is a function
of the number of (X–Y-G) repeat units in each CLP strand [87], the identity of the
amino acids located at the X and Y positions [82, 86], and solvent quality [88]. As a
result, CLPs have been used in several biomedical applications such as drug delivery
and tissue engineering due to their thermal stability, biocompatibility, and ability to
recapitulate the mechanical and chemical properties of the ECM [89–93].
There have been a significant number of studies aimed at relating the composition of CLPs to the triple helix stability and melting temperature. For example, it
is accepted that CLPs containing hydroxyproline, O, have higher melting temperatures than CLPs which lack hydroxyproline. Persikov et al. used a host–guest peptide
system to investigate the amino acid propensities for the collagen triple helix [94].
Using circular dichroism spectroscopy, they showed that the most stable residues
in the Y position of (X–Y-G) amino acid triplets are Hyp and Arg while the most
stabilizing residue in the X position is Pro. Short collagen-like sequences comprising
fewer than ten (X–Y-G) amino acid triplets have also been crystallized and characterized via experimental and computational approaches [84, 95–97]. All-atom MD
simulations of (POG) 4 (POA)(POG) 4 by Klein and Huang showed that waters occupying the water bridge h-bonds were not tightly bound, which led them to assert that
collagen’s extra stability does not arise from h-bonding mediated by a network of
bridging waters [95]. Other studies have also shown that hydroxyproline’s stabilizing
effect has been attributed to stereoelectronic effects rather than its ability to partake
in water-mediated h-bonding. These stereoelectronic effects involve gauche and n
→ π * interactions which pre-organize the collagen backbone such that each peptide
chain adopts the correct backbone dihedral angles for the PPII helix conformation
[82, 83]. Other computational studies have also focused on the mechanical properties
of CLPs such as their elastic moduli. Gautieri et al. conducted atomistic MD simulations of CLPs containing glycine mutations and showed that these mutated peptides
display softer mechanical properties than wild-type tropocollagen molecules [96,
97]. These results have important implications for diseases such as Osteogenesis
Imperfecta where glycine mutations in type I collagen genes can lead to a loss of
structural integrity of the body’s tissues and in some cases, even prenatal death.
Besides the above studies describing the effect of hydroxyproline and glycine
mutations on the thermal and mechanical stability of CLP triple helices, there have
also been several computational studies focused on the effects of sequence length
[98], amino acid substitutions [99] and amino acid stereochemistry [100] (i.e., L
versus D isomers) specifically on the thermal stability of the CLP triple helix. Raman
et al. performed all-atom MD simulations of two host–guest peptides designed by
replacing aspartic acid in the X and Y positions of (GPO)-based CLPs [99]. They
showed that aspartic acid when located at the Y position (i.e., GPD) destabilizes the