Decoding Collagen Triple Helix Stability by Means of Hybrid DFT Simulations

Association between N-Terminal Pyrenes Stabilizes the Collagen Triple Helix

Collagen model peptides featuring the fluorophore pyrene at their N-termini have been synthesized, and their thermal denaturation has been examined using circular dichroism (CD) and fluorescence spectroscopies. Flanking the (Pro-Hyp-Gly)7 core of the peptide monomers at positions 1 and/or 23 in the primary sequence, Lys residues were introduced to ensure water solubility. Triple helices derived from such peptides show a broad excimer emission at ∼480 nm, indicative of interaction between the pyrene units. CD experiments show that the fluorophores enhance helix stability primarily through entropic effects. Unfolding temperatures (Tm) increase by up to 7 °C for systems with N-terminal lysine residues and by up to 21 °C for systems in which the first-position Lys is replaced by Ala. Tm values derived from fluorescence measurements (at 50 μM) typically lie within ∼1 °C of those obtained using CD (at 200 μM). Computational modeling in a water continuum using B3LYP-GD3 and M06-2X functionals predicts that face-to-face association of fluorophores can occur while H-bonding within the [(POG)n]3 assembly is retained. Such parallel stacking is consistent with hydrophobically driven stabilization. Labeling collagen peptides with pyrene is a synthetically simple way to promote triple helicity while providing a means to obtain Tm data on relatively dilute samples.

Chemical bonds in collagen rupture selectively under tensile stress

Collagen fibres are the main constituent of the extracellular matrix, and fulfil an important role in the structural stability of living multicellular organisms. An open question is how collagen absorbs pulling forces, and if the applied forces are strong enough to break bonds, what mechanisms underlie this process. As experimental studies on this topic are challenging, simulations are an important tool to further our understanding of these mechanisms. Here, we present pulling simulations of collagen triple helices, revealing the molecular mechanisms induced by tensile stress. At lower forces, pulling alters the configuration of proline residues leading to an effective absorption of applied stress. When forces are strong enough to introduce bond ruptures, these are located preferentially in X-position residues. Reduced backbone flexibility, for example through mutations or cross linking, weakens tensile resistance, leading to localised ruptures around these perturbations. In fibre-like segments, a significant overrepresentation of ruptures in proline residues compared to amino acid contents is observed. This study confirms the important role of proline in the structural stability of collagen, and adds detailed insight into the molecular mechanisms underlying this observation.

Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling

Cellulose/collagen composites have been widely used in biomedicine and tissue engineering. Interfacial interactions are crucial in determining the final properties of cellulose/collagen composite. Molecular dynamics simulations were carried out to gain insights into the interactions between cellulose and collagen. It has been found that the structure of collagen remained intact during adsorption. The results derived from umbrella sampling showed that (110) and ([Formula: see text]) faces exhibited the strongest affinity with collagen (100) face came the second and (010) the last, which could be attributed to the surface roughness and hydrogen-bonding linkers involved water molecules. Cellulose planes with flat surfaces and the capability to form hydrogen-bonding linkers produce stronger affinity with collagen. The occupancy of hydrogen bonds formed between cellulose and collagen was low and not significantly contributive to the binding affinity. These findings provided insights into the interactions between cellulose and collagen at the molecular level, which may guide the design and fabrication of cellulose/collagen composites.

Nanoscale MXene Interlayer and Substrate Adhesion for Lubrication: A Density Functional Theory Study

Understanding the interlayer interaction at the nanoscale in two-dimensional (2D) transition metal carbides and nitrides (MXenes) is important to improve their exfoliation/delamination process and application in (nano)-tribology. The layer-substrate interaction is also essential in (nano)-tribology as effective solid lubricants should be resistant against peeling-off during rubbing. Previous computational studies considered MXenes' interlayer coupling with oversimplified, homogeneous terminations while neglecting the interaction with underlying substrates. In our study, Ti-based MXenes with both homogeneous and mixed terminations are modeled using density functional theory (DFT). An ad hoc modified dispersion correction scheme is used, capable of reproducing the results obtained from a higher level of theory. The nature of the interlayer interactions, comprising van der Waals, dipole-dipole, and hydrogen bonding, is discussed along with the effects of MXene sheet's thickness and C/N ratio. Our results demonstrate that terminations play a major role in regulating MXenes' interlayer and substrate adhesion to iron and iron oxide and, therefore, lubrication, which is also affected by an external load. Using graphene and MoS₂ as established references, we verify that MXenes' tribological performance as solid lubricants can be significantly improved by avoiding -OH and -F terminations, which can be done by controlling terminations via post-synthesis processing.

The effects of glycine to alanine mutations on the structure of GPO collagen model peptides

Collagen proteins are the main constituents of the extracellular matrix (ECM), and fulfil a number of wide-ranging functions, including contributions to the mechanical and biological behaviour of the ECM. Due to the heterogeneous nature of collagen in tissue samples it is difficult to fully explain the experimental observation, and hence the study of shorter model peptides is common place. Here, the computational energy landscape framework is employed to study Gly to Ala mutations in a GPO model peptide. The results show good agreement with the experimental observations for the GPO reference and a triply mutated peptide, demonstrating the validity of the approach. The modelling predicts that changes in structure are moderate and localised, with an increased dynamic in the backbone and alterations to the hydrogen bonding pattern. Two mechanisms for adjusting to the mutations are observed, with potential consequences regarding protein binding. Finally, in line with a hypothesis that proline puckering allows controlled flexibility (Chow et al., Sci. Rep., 2018, 8, 13809), alterations in the puckering preferences are observed in the strained residues surrounding the mutational sites.

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach

Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO₂ (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO₂ surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO₂ surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.

Infrared harmonic features of collagen models at B3LYP-D3: From amide bands to the THz region

In this paper, we have studied the vibrational spectral features for the collagen triple helix using a dispersion corrected hybrid density functional theory (DFT-D) approach. The protein is simulated by an infinite extended polymer both in the gas phase and in a water micro-solvated environment. We have adopted proline-rich collagen models in line with the high content of proline in natural collagens. Our scaled harmonic vibrational spectra are in very good agreement with the experiments and allow for the peak assignment of the collagen amide I and III bands, supporting or questioning the experimental interpretation by means of vibrational normal modes analysis. Furthermore, we demonstrated that IR spectroscopy in the THz region can detect the small variations inherent to the triple helix helicity (10/3 over 7/2), thus elucidating the packing state of the collagen. So far, identifying the collagen helicity is only possible by means of crystal x-ray diffraction.

Balancing Cost and Accuracy in Quantum Mechanical Simulations on Collagen Protein Models

Collagen proteins are spread in almost every vertebrate's tissue with mechanical function. The defining feature of this fundamental family of proteins is its well-known collagen triple-helical domain. This helical domain can have different geometries, varying in helical elongation and interstrands contact, as a function of the amino acidic composition. The helical geometrical features play an important role in the interaction of the collagen protein with cell receptors, but for the vast majority of collagen compositions, these geometrical features are unknown. Quantum mechanical (QM) simulations based on the density functional theory (DFT) provide a robust approach to characterize the scenario on the collagen composition-structure relationships. In this work, we analyze the role of the adopted computational method in predicting the collagen structure for two purposes. First, we look for a cost-effective computational approach to apply to a large-scale composition-structure analysis. Second, we attempt to assess the robustness of the predictions by varying the QM methods. Therefore, we have run geometry optimization on periodic models of the collagen protein using a variety of approaches based on the most commonly used DFT functionals (PBE, HSE06, and B3LYP) with and without dispersion correction (D3^ABC). We have coupled these methods with several different basis sets, looking for the highest accuracy/cost ratio. Furthermore, we have studied the performance of the composite HF-3c method and the semiempirical GFN1-xTB method. Our results identify a computational recipe that is potentially capable of predicting collagen structural features in line with DFT simulations, with orders of magnitude reduced computational cost, encouraging further investigations on the topic.

Insertion of Pro-Hyp-Gly provides 2 kcal mol-1 stability but attenuates the specific assembly of ABC heterotrimeric collagen triple helices

Collagen is a major structural component of the extracellular matrix and connective tissue. The key structural feature of collagen is the collagen triple helix, with a Xaa-Yaa-Gly (glycine) repeating pattern. The most frequently occurring triplet is Pro (proline)-Hyp (hydroxyproline)-Gly. The reversible thermal folding and unfolding of a series of heterotrimeric collagen triple helices with varying number of Pro-Hyp-Gly triplets were monitored by circular dichroism spectroscopy to determine the unfolding thermodynamic parameters Tm (midpoint transition temperature), ΔHTm (unfolding enthalpy), and ΔGunfold (unfolding free energy). The Tm and ΔGunfold of the heterotrimeric collagen triple helices increased with increasing number of Pro-Hyp-Gly triplets. The ΔGunfold increased by 2.0 ± 0.2 kcal mol-1 upon inserting one Pro-Hyp-Gly triplet into all three chains. The Tm difference between the most stable ABC combination and the second most stable BCC combination decreased with increasing number of Pro-Hyp-Gly triplets, even though the ΔGunfold difference remained the same. These results should be useful for tuning the stability of collagen triple helical peptides for hydrogel formation, recognition of denatured collagen triple helices as diagnostics and therapeutics, and targeted drug delivery.

Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence

Establishing the “Materials 4.0” paradigm requires intimate knowledge of the virtual space in materials design.

Elucidating the Nature of Interactions in Collagen Triple-Helix Wrapping

Collagen is the most abundant protein family in the animal kingdom. Its structural motif envisages three polypeptide chains coiled in the so-called collagen triple helix. Depending on the triplet amino acid sequence of the chains, collagen has different helical arrangements. Such atomic-scale structural variations have a large impact on the large-scale structure of collagen. In this Letter, we elucidate the interactions that are responsible for a specific helical pattern of the collagen protein by means of DFT-D-based computer simulations. We demonstrate that interchain interactions and solvation effects stabilize compact helices over elongated ones. Conversely, elongated helices are stabilized by less geometrical strain and entropic factors. Our computational procedure predicts the collagen helical pattern in agreement with the experimental evidence.