Proline puckering parameters for collagen structure simulations

Wu, Di

doi:10.1063/1.4915295

Cited by 5 publications

(2 citation statements)

References 38 publications

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“…This peptide was chemically synthesized, and its X-ray diffraction was taken at 1.30 Å resolution [17]. It was previously studied for properties such as stability and solvation of collagen protein [31,36,37]. The unit cell consisted of two head-to-tail triple helices, of which we focused on one (chains A, B, and C).…”

Section: Methodsmentioning

confidence: 99%

Collagen Structured Hydration

Biswal,

Agmon

2023

Biomolecules

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Collagen is a triple-helical protein unique to the extracellular matrix, conferring rigidity and stability to tissues such as bone and tendon. For the [(PPG)10]3 collagen-mimetic peptide at room temperature, our molecular dynamics simulations show that these properties result in a remarkably ordered first hydration layer of water molecules hydrogen bonded to the backbone carbonyl (bb-CO) oxygen atoms. This originates from the following observations. The radius of gyration attests that the PPG triplets are organized along a straight line, so that all triplets (excepting the ends) are equivalent. The solvent-accessible surface area (SASA) for the bb-CO oxygens shows a repetitive regularity for every triplet. This leads to water occupancy of the bb-CO sites following a similar regularity. In the crystal-phase X-ray data, as well as in our 100 K simulations, we observe a 0-2-1 water occupancy in the P-P-G triplet. Surprisingly, a similar (0-1.7-1) regularity is maintained in the liquid phase, in spite of the sub-nsec water exchange rates, because the bb-CO sites rarely remain vacant. The manifested ordered first-shell water molecules are expected to produce a cylindrical electrostatic potential around the peptide, to be investigated in future work.

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Section: Methodsmentioning

confidence: 99%

Collagen Structured Hydration

Biswal,

Agmon

2023

Biomolecules

View full text Add to dashboard Cite

show abstract

“…It was chemically synthesized, and its X-ray diffraction was taken at 1.30 Å resolution [16]. This peptide system has been extensively studied for properties such as stability and solvation of collagen protein [30,36,37]. The unit cell consisted of two head-to-tail triple helices, of which we focused on one (chains A, B and C).…”

Section: Methodsmentioning

confidence: 99%

Collagen Structured Hydration

Biswal,

Agmon

2023

Preprint

View full text Add to dashboard Cite

Collagen is a triple-helical protein unique to the extracellular matrix, conferring rigidity and stability to tissues such as bone and tendon. For the [(PPG)10]3 collagen-mimetic peptide at room temperature, our molecular dynamics simulations show that these properties result in a remarkably ordered first hydration layer, of water molecules hydrogen-bonded to the backbone-carbonyl (bb-CO) oxygen atoms. This originates from the following observations. The radius of gyration attests that the PPG triplets are organized along a straight line, so that all triplets (excepting the ends) are equivalent. The solvent accessible surface area (SASA) for the bb-CO oxygens shows a repetitive regularity for every triplet. This leads to bb-CO⋯HOH occupancy following a similar regularity, similar also to the crystal-phase 0-2-1 water occupancy in the P-P-G triplet. The regularity is maintained in spite of the sub-nsec water exchange rate, because the bb-CO sites rarely remain vacant. The manifested ordered first-shell water molecules are expected to produce a cylindrical electrostatic potential around the peptide, that might guide cation diffusion in its vicinity.

show abstract