Non-linearity of the collagen triple helix in solution and implications for collagen function

Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly)n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units. In addition, one unblocked peptide, (POG)10unblocked, was compared with the blocked (POG)10 as a control for the significance of end effects. Complementary analytical ultracentrifugation and synchrotron small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures for each of the helices. These structures were fitted against their respective scattering data to reveal the best fitting structures from this large ensemble of possible helix structures. This curve fitting confirmed a small degree of non-linearity to exist in these best fit triple helices, with the degree of bending approximated as 4–17° from linearity. Our results open the way for further studies of other collagen triple helices with different sequences and stabilities in order to clarify the role of molecular rigidity and flexibility in collagen extracellular and immune function and disease.

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The solution structures of native and patient monomeric human IgA1 reveal asymmetric extended structures: implications for function and IgAN disease

Biochemical Journal ◽

10.1042/bj20150612 ◽

2015 ◽

Vol 471 (2) ◽

pp. 167-185 ◽

Cited By ~ 13

Author(s):

Gar Kay Hui ◽

David W. Wright ◽

Owen L. Vennard ◽

Lucy E. Rayner ◽

Melisa Pang ◽

...

Keyword(s):

Neutron Scattering ◽

Receptor Binding ◽

Analytical Ultracentrifugation ◽

Scattering Data ◽

X Ray ◽

Solution Structures ◽

Binding Function ◽

Atomistic Modelling ◽

Modelling Approach

Detailed analytical ultracentrifugation and X-ray/neutron scattering data and a new atomistic modelling approach revealed asymmetric extended solution structures for human IgA1 that account for its receptor-binding function. IgA1 with different hinge O-galactosylation patterns showed similar structures.

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The solution structures of higher-order human telomere G-quadruplex multimers

Nucleic Acids Research ◽

10.1093/nar/gkaa1285 ◽

2021 ◽

Vol 49 (3) ◽

pp. 1749-1768

Author(s):

Robert C Monsen ◽

Srinivas Chakravarthy ◽

William L Dean ◽

Jonathan B Chaires ◽

John O Trent

Keyword(s):

Analytical Ultracentrifugation ◽

Persistence Length ◽

Md Simulations ◽

Size Exclusion ◽

Scattering Data ◽

Solution Structures ◽

X Ray Scattering ◽

G Quadruplex ◽

Dynamics Simulations ◽

Global Fitting

Abstract Human telomeres contain the repeat DNA sequence 5′-d(TTAGGG), with duplex regions that are several kilobases long terminating in a 3′ single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate models proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5′-d(TTAGGG)n, with n = 8, 12 and 16, fold into multimeric structures containing the maximal number (2, 3 and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of ∼34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.

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The solution structures of higher-order human telomere G-quadruplex multimers

10.1101/2020.11.13.382036 ◽

2020 ◽

Author(s):

Robert C. Monsen ◽

Srinivas Chakravarthy ◽

William L. Dean ◽

Jonathan B. Chaires ◽

John O. Trent

Keyword(s):

Analytical Ultracentrifugation ◽

Persistence Length ◽

Md Simulations ◽

Size Exclusion ◽

Scattering Data ◽

Solution Structures ◽

X Ray Scattering ◽

G Quadruplex ◽

Dynamics Simulations ◽

Global Fitting

ABSTRACTHuman telomeres contain the repeat DNA sequence 5’(TTAGGG), with duplex regions that are several kilobases long terminating in a 3’ single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate modes proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5’(TTAGGG)n, with n=8, 12, and 16, fold into multimeric structures containing the maximal number (2, 3, and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of about 34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.

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Ultrafast calculation of diffuse scattering from atomistic models

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273318015632 ◽

2019 ◽

Vol 75 (1) ◽

pp. 14-24 ◽

Cited By ~ 6

Author(s):

Joseph A. M. Paddison

Keyword(s):

Diffuse Scattering ◽

Large Data ◽

Large Data Sets ◽

Scattering Data ◽

Frequency Noise ◽

Data Sets ◽

Fast Method ◽

Crystalline Materials ◽

Atomistic Models ◽

Dynamics Simulations

Diffuse scattering is a rich source of information about disorder in crystalline materials, which can be modelled using atomistic techniques such as Monte Carlo and molecular dynamics simulations. Modern X-ray and neutron scattering instruments can rapidly measure large volumes of diffuse-scattering data. Unfortunately, current algorithms for atomistic diffuse-scattering calculations are too slow to model large data sets completely, because the fast Fourier transform (FFT) algorithm has long been considered unsuitable for such calculations [Butler & Welberry (1992). J. Appl. Cryst. 25, 391–399]. Here, a new approach is presented for ultrafast calculation of atomistic diffuse-scattering patterns. It is shown that the FFT can actually be used to perform such calculations rapidly, and that a fast method based on sampling theory can be used to reduce high-frequency noise in the calculations. These algorithms are benchmarked using realistic examples of compositional, magnetic and displacive disorder. They accelerate the calculations by a factor of at least 102, making refinement of atomistic models to large diffuse-scattering volumes practical.

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Structural diversity and domain composition of a unique collagenous fragment (intima collagen) obtained from human placenta

Biochemical Journal ◽

10.1042/bj2110295 ◽

1983 ◽

Vol 211 (2) ◽

pp. 295-302 ◽

Cited By ~ 97

Author(s):

E Odermatt ◽

J Risteli ◽

V van Delden ◽

R Timpl

Keyword(s):

Human Placenta ◽

Triple Helix ◽

Structural Diversity ◽

Helical Conformation ◽

Basic Unit ◽

Bacterial Collagenase ◽

Disulphide Bonds ◽

Triple Helices ◽

Electron Microscopical ◽

Polypeptide Chains

Intima collagen was obtained from pepsin digests of human placenta in two forms, which differ to some extent in the size of their constituent polypeptide chains (Mr 50 000-70 000). These chains are connected by disulphide bonds to large aggregates. The aggregates are arranged in a triple-helical conformation with a remarkably high thermal stability (Tm 41-62 degrees C) and are resistant to further proteolytic digestion. Reduction of as little as 5% of the disulphide bonds produces mainly monomeric triple helices (Mr about 160 000) with Tm 32 degrees C. Partially reduced material can be separated into triple-helical and non-collagenous domains by proteolysis. Pepsin releases a collagenous component with chains of Mr 38 000. Bacterial collagenase liberates two non-collagenous segments (Mr 15 000-30 000) rich in cystine. Treatment with collagenase before reduction separates intima collagen into a large fragment composed of collagenous (Tm 41 degrees C) and non-collagenous structures and a single non-collagenous segment. The data support the electron-microscopical model of intima collagen [Furthmayr, Wiedemann, Timpl, Odermatt & Engel (1983) Biochem. J. 211, 303-311], indicating that the basic unit of the fragment consists of a continuous triple helix joining two globular domains.

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Atomistic modelling to better understand neutron scattering data

Neutron News ◽

10.1080/10448632.2012.695720 ◽

2012 ◽

Vol 23 (3) ◽

pp. 2-4

Author(s):

Mark Johnson ◽

Don Kearley

Keyword(s):

Neutron Scattering ◽

Scattering Data ◽

Atomistic Modelling

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An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/d0cp04672h ◽

2020 ◽

Vol 22 (48) ◽

pp. 28055-28073

Author(s):

Anupamjeet Kaur ◽

Deepti Goyal ◽

Bhupesh Goyal

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Helical Conformation ◽

Aβ Peptide ◽

Α Helix ◽

Dynamics Simulations

The molecular dynamics simulations highlighted that ADH-31 inhibited Aβ42 aggregation by constraining Aβ peptide into helical conformation and destabilized Aβ42 trimer as well as protofibril structures.

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