A simulation study on the significant nanomechanical heterogeneous properties of collagen

Establishment of a targeted proteomics method for the quantification of collagen chain: Revealing the chain stoichiometry of heterotypic collagen fibrils in sea cucumber

Collagen is the most abundant and important structural biomacromolecule in sea cucumbers. The sea cucumber collagen fibrils were previously confirmed to be heterotypic, nevertheless, the stoichiometry of collagen α-chains governing the complexity of collagen fibrils is still poorly understood. Herein, four representative collagen α-chains in sea cucumber including two clade A fibrillar collagens, one clade B fibrillar collagen, and one fibril-associated collagen with interrupted triple helices were selected. After the screening of signature peptides and optimization of multiple reaction monitoring (MRM) acquisition parameters including fragmentation, collision energy, and ion transition, a feasible MRM-based method was established. Consequently, the stoichiometry of the four collagen chains was determined to be approximately 100:54:3:4 based on the method. The assembly forms of sea cucumber collagen fibrils were further hypothesized according to the chain stoichiometry. This study facilitated the quantification of collagen and understanding of the collagen constituents in sea cucumber.

Unraveling the molecular mechanism of collagen flexibility during physiological warmup using molecular dynamics simulation and machine learning

Physiological warmup plays an important role in reducing the injury risk in different sports. In response to the associated temperature increase, the muscle and tendon soften and become easily stretched. In this study, we focused on type I collagen, the main component of the Achilles tendon, to unveil the molecular mechanism of collagen flexibility upon slight heating and to develop a model to predict the strain of collagen sequences. We used molecular dynamics approaches to simulate the molecular structures and mechanical behavior of the gap and overlap regions in type I collagen at 307 K, 310 K, and 313 K. The results showed that the molecular model in the overlap region is more sensitive to temperature increases. Upon increasing the temperature by 3 degrees Celsius, the end-to-end distance and Young's modulus of the overlap region decreased by 5% and 29.4%, respectively. The overlap region became more flexible than the gap region at higher temperatures. GAP-GPA and GNK-GSK triplets are critical for providing molecular flexibility upon heating. A machine learning model developed from the molecular dynamics simulation results showed good performance in predicting the strain of collagen sequences at a physiological warmup temperature. The strain-predictive model could be applied to future collagen designs to obtain desirable temperature-dependent mechanical properties.

The Role of the Extrafibrillar Volume on the Mechanical Properties of Molecular Models of Mineralized Bone Microfibrils

Bones are responsible for body support, structure, motion, and several other functions that enable and facilitate life for many different animal species. They exhibit a complex network of distinct physical structures and mechanical properties, which ultimately depend on the fraction of their primary constituents at the molecular scale. However, the relationship between structure and mechanical properties in bones are still not fully understood. Here, we investigate structural and mechanical properties of all-atom bone molecular models composed of type-I collagen, hydroxyapatite (HA), and water by means of fully atomistic molecular dynamics simulations. Our models encompass an extrafibrillar volume (EFV) and consider mineral content in both the EFV and intrafibrillar volume (IFV), consistent with experimental observations. We investigate solvation structures and elastic properties of bone microfibril models with different degrees of mineralization, ranging from highly mineralized to weakly mineralized and nonmineralized models. We find that the local tetrahedral order of water is lost in similar ways in the EFV and IFV regions for all HA containing models, as calcium and phosphate ions are strongly coordinated with water molecules. We also subject our models to tensile loads and analyze the spatial stress distribution over the nanostructure of the material. Our results show that both mineral and water contents accumulate significantly higher stress levels, most notably in the EFV, thus revealing that this region, which has been only recently incorporated in all-atom molecular models, is fundamental for studying the mechanical properties of bones at the nanoscale. Furthermore, our results corroborate the well-established finding that high mineral content makes bone stiffer.

Mechanics of isolated individual collagen fibrils

Collagen fibrils are the fundamental structural elements in vertebrate animals and compose a framework that provides mechanical support to load-bearing tissues. Understanding how these fibrils initially form and mechanically function has been the focus of a myriad of detailed investigations over the last few decades. From these studies a great amount of knowledge has been acquired as well as a number of new questions to consider. In this review, we examine the current state of our knowledge of the mechanical properties of extant fibrils. We emphasize on the mechanical response and related deformation of collagen fibrils upon tension, which is the predominant load imposed in most collagen-rich tissues. We also illuminate the gaps in knowledge originating from the intriguing results that the field is still trying to interpret. STATEMENT OF SIGNIFICANCE: : Collagen is the result of millions of years of biological evolution and is a unique family of proteins, the majority of which provide mechanical support to biological tissues. Cells produce collagen molecules that self-assemble into larger structures, known as collagen fibrils. As simple as they appear under an optical microscope, collagen fibrils display a complex ultrastructural architecture tuned to the external forces that are imposed upon them. Even more complex is the way collagen fibrils deform under loading, and the nature of the mechanisms that drive their formation in the first place. Here, we present a cogent synthesis of the state-of-knowledge of collagen fibril mechanics. We focus on the information we have from in vitro experiments on individual, isolated from tissues, collagen fibrils and the knowledge available from in silico tests.

Devising Bone Molecular Models at the Nanoscale: From Usual Mineralized Collagen Fibrils to the First Bone Fibers Including Hydroxyapatite in the Extra-Fibrillar Volume

At the molecular scale, bone is mainly constituted of type-I collagen, hydroxyapatite, and water. Different fractions of these constituents compose different composite materials that exhibit different mechanical properties at the nanoscale, where the bone is characterized as a fiber, i.e., a bundle of mineralized collagen fibrils surrounded by water and hydroxyapatite in the extra-fibrillar volume. The literature presents only models that resemble mineralized collagen fibrils, including hydroxyapatite in the intra-fibrillar volume only, and lacks a detailed prescription on how to devise such models. Here, we present all-atom bone molecular models at the nanoscale, which, differently from previous bone models, include hydroxyapatite both in the intra-fibrillar volume and in the extra-fibrillar volume, resembling fibers in bones. Our main goal is to provide a detailed prescription on how to devise such models with different fractions of the constituents, and for that reason, we have made step-by-step scripts and files for reproducing these models available. To validate the models, we assessed their elastic properties by performing molecular dynamics simulations that resemble tensile tests, and compared the computed values against the literature (both experimental and computational results). Our results corroborate previous findings, as Young’s Modulus values increase with higher fractions of hydroxyapatite, revealing all-atom bone models that include hydroxyapatite in both the intra-fibrillar volume and in the extra-fibrillar volume as a path towards realistic bone modeling at the nanoscale.

Deformation Mechanisms of "Two-Part" Natural Adhesive in Bone Interfibrillar Nano-Interfaces

Noncollagenous proteins at nanoscale interfaces in bone are less than 2-3% of bone content by weight, while they contribute more than 30% to fracture toughness. Major gaps in quantitative understanding of noncollagenous proteins' role in the interfibrillar interfaces, largely because of the limitation of probing their nanoscale dimension, have resulted in ongoing controversies and several outstanding hypotheses on their role and function, arguably going back to centuries ago to the original work from Galileo. Our results from the first detailed computational model of the nano-interface in the bone reveal "synergistic" deformation mechanism of a "double-part" natural glue, that is, noncollagenous osteopontin and osteocalcin at the interfibrillar interface. Specifically, through strong anchoring and formation of dynamic binding sites on mineral nanoplatelets, the nano-interface can sustain a large nonlinear deformation with ductility approaching 5000%. This large deformation results in an outstanding specific energy to failure exceeding ∼350 J/g, which is larger than the most known tough materials (such as Kevlar, spider silk, and so forth.).

Steered molecular dynamics characterization of the elastic modulus and deformation mechanisms of single natural tropocollagen molecules

Collagen is a common structural protein, providing mechanical integrity for various vertebrate connective tissues such as cartilage and bone. The mechanical behaviours of these tissues under physical stimulations are controlled by the hierarchical structure of collagen and its interactions with other extracellular matrix molecules. However, the mechanical properties and deformation mechanisms of natural collagen under physiological loading rates at the molecular level are not fully understood. In this study, comprehensive steered molecular dynamics (SMD) simulations were performed on the 2nd intact overlap region (d2ol) and the 2nd intact D-period (d2olgp) of an in-situ characterized collagen molecule, under a large range of strain rates (6.5 × 10⁶% s^-1 to 1.3 × 10¹²% s^-1). The results show that, depending on the applied strain rates, tropocollagen molecules unfold in different ways. Particularly, at high and intermediate strain rates, the number of inter-chain hydrogen bonds decreases rapidly even at small deformations, leading to a dramatic increase in the force. This results in an increase in the estimated Young's modulus of collagen triple helices as the deformation rate goes up, which, together with the nonlinear mechanical behaviour, explains the broad range of the Young's modulus for collagen model peptides reported in earlier SMD studies. Atomistic-level analyses indicate that the elastic modulus of single tropocollagen molecules decreases as the strain rate becomes smaller. However, for strain rates below 1.3 × 10⁸% s^-1, the tangent Young's modulus of d2ol (d2olgp) converges to approximately 3.2 GPa (3.4 GPa), at the strain of 10.5% (12%) when the segment is fully uncrimped. Furthermore, for strain rates under 1.3 × 10⁸% s^-1, d2ol and d2olgp show identical deformation mechanisms (unwinding, uncoiling and backbone stretching), but the corresponding strain ranges are different. This study will aid in future studies on characterizing the mechanical properties of collagen molecules and collagen-like peptides by indicating the proper pulling strain rates and how to determine the suitable strain range used for evaluating the elastic modulus.

Clustering of hydroxyapatite on a super-twisted collagen microfibril under mechanical tension

Atomistic simulation of biomineralization of a super-twisted collagen microfibril reveals that mechanical stimulation facilitates clustering and growth of hydroxyapatite onto collagen.