The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study

Marlowe, Ashley E.; Singh, Abhishek; Yingling, Yaroslava G.

doi:10.1016/j.msec.2012.07.044

Cited by 13 publications

(9 citation statements)

References 38 publications

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“…In our simulations, we used optimised parameters that will play a key role in generating realistic results, where the derivation of these parameters requires trial-and-error runs (73). Following the logistics from our previous works (74), the best combinations of force (kcal/mol) and velocity (Å/time step) values were selected, where a spring constant of 0.1 kcal/mol/Å 2 and a pull rate of 0.05 fN per a 2 fsec simulation timestep or a vector heading from the entrance of the pore to the opposite side of the pore. Using this pulling force, it was confirmed for the HvNIP2;1 model and the SoPIP2;1 crystal structure that these AQPs exhibited water transporting characteristics (Fig.…”

Section: Discussionmentioning

confidence: 99%

Barley HvNIP2;1 aquaporin permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification

Venkataraghavan¹,

Kim

Schwerdt³

et al. 2023

Preprint

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Aquaporins can facilitate the passive movement of water and small polar molecules and some ions. The barley Nodulin 26-like Intrinsic Protein (HvNIP2;1) embedded in liposomes and examined through stopped-flow light scattering spectrophotometry and Xenopus oocyte swelling assays was found to permeate water, boric and germanic acids, sucrose and L-arabinose but not D-glucose or D-fructose. Other saccharides, such as neutral (D-mannose, D-galactose, D-xylose, D-mannoheptaose) and charged (N-acetyl D-glucosamine, D-glucosamine, D-glucuronic acid) aldoses, disaccharides (lactose, cellobiose, gentiobiose, trehalose), trisaccharide raffinose, and urea, glycerol, and acyclic polyols were permeated to a much lower extent. Apparent permeation of hydrated KCl and MgSO4 ion pairs was observed, while CH3COONa and NaNO3 permeated at significantly lower rates. Experiments with boric acid and sucrose revealed no apparent interaction between solutes when permeated together, and AgNO3 blocked the permeation of all solutes. Full-scale steered molecular dynamics simulations of HvNIP2;1 and spinach SoPIP2;1 revealed possible rectification for water, boric acid, and sucrose transport, and defined key residues interacting with permeants. In a biological context, the simulated sucrose rectification could mediate its apoplastic-to-intracellular transport but not the reverse, thus, constituting a novel element of plant saccharide-transporting machinery. Phylogenomic analyses of 164 Viridiplantae and 2,993 Archaean, bacterial, fungal, and Metazoan aquaporins rationalised solute poly-selectivity in NIP3 sub-clade entries and suggested that they diversified from other sub-clades to acquire a unique specificity of saccharide transporters. Solute specificity definition in NIP aquaporins could inspire developing plants for sustained food production.

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Section: Discussionmentioning

confidence: 99%

Barley HvNIP2;1 aquaporin permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification

Venkataraghavan¹,

Kim

Schwerdt³

et al. 2023

Preprint

Self Cite

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“…Coulombic potentials were calculated using the Particle Mesh Ewald summation with a cut-off radius of 8.0 Å. An 8.0 Å cut-off was chosen due to the dense fibrillar environment of the collagen molecule within the fibril, which is consistent with many previous modelling studies on fibrillar collagen; the energies converge within the timescale of the simulation (Collier et al, 2015;Klein & Huang, 1999;Marlowe, Singh, & Yingling, 2012;Streeter & de Leeuw, 2010). A time step of 2 fs was adopted for all MD simulations and hydrogen-bond lengths were constrained using the SHAKE algorithm (Ryckaert, Ciccotti, & Berendsen, 1977).…”

Section: Fibrillar Collagen Simulations Detailmentioning

confidence: 99%

Relative orientation of collagen molecules within a fibril: a homology model forhomo sapienstype I collagen

Collier

Nash

Birch³

et al. 2018

Journal of Biomolecular Structure and Dynamics

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Type I collagen is an essential extracellular protein that plays an important structural role in tissues that require high tensile strength. However, owing to the molecule's size, to date no experimental structural data are available for the Homo sapiens species. Therefore, there is a real need to develop a reliable homology model and a method to study the packing of the collagen molecules within the fibril. Through the use of the homology model and implementation of a novel simulation technique, we have ascertained the orientations of the collagen molecules within a fibril, which is currently below the resolution limit of experimental techniques. The longitudinal orientation of collagen molecules within a fibril has a significant effect on the mechanical and biological properties of the fibril, owing to the different amino acid side chains available at the interface between the molecules.

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“…Assembling proteins as well as ordered linear aggregates, defined as fibrils, has attracted more attention in recent years. These linear protein fibrils can have a good potential as materials in thickening or gelling, which are widely used in beverage, dessert, and sausage [3][4][5][6][7].…”

Section: Introductionmentioning

confidence: 99%

“…Generally, electrostatic repulsive forces attenuated gradually at the high ionic strength, and the preponderant intermolecular hydrophobic forces induced formation of clustered aggregates. Contrarily, at low ionic strength and pH, electrostatic repulsive force predominates the aggregates morphology and formed linear fibrils [7,11,12]. At low pH and low ionic strength, the gels have many advantages, for example, being transparent or semitransparent, being more elastic, and being of low gel critical concentration [13].…”

Section: Introductionmentioning

confidence: 99%

Self‐Assembly of Rice Bran Globulin Fibrils in Electrostatic Screening: Nanostructure and Gels

Huang

Zhang²,

2014

Journal of Nanomaterials

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The effects of various ionic strengths and protein concentrations on the fibrils structure and gel properties of rice bran globulin (RBG) at pH 2.0 were investigated using atomic force microscopy (AFM), rheometer, and scanning electron microscope (SEM). AFM images showed the morphology of assembling RBG fibrils from strand beads to becoming branch clustered, when electrostatic repulsive forces attenuated gradually with increasing ionic strength. NaCl seems to accelerate the kinetics of fibrils formation, resulting in a significant increase in Th T fluorescence intensity. The increased ionic strengths promote particle size increasing and zeta potential decreasing synchronously. The percolation modelG'~C-Cpnbe used to calculate theoretical RBG gels concentration at various ionic strengths (0–500 mM), which decreased from 15.17 ± 0.63 to 2.26 ± 0.27 wt%. SEM images exhibited a granular mesh-like gel structure. A more homogenous structure occurred in low ionic strength. This study elucidates properties of RBG fibrils and gels as a bioactive material.

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The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study

Cited by 13 publications

References 38 publications

Barley HvNIP2;1 aquaporin permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification

Barley HvNIP2;1 aquaporin permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification

Relative orientation of collagen molecules within a fibril: a homology model forhomo sapienstype I collagen

Self‐Assembly of Rice Bran Globulin Fibrils in Electrostatic Screening: Nanostructure and Gels

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