Molecular dynamics simulations on networks of heparin and collagen

Molecular interplay of ADAMTS13-MDTCS and von willebrand Factor-A2: deepened insights from extensive atomistic simulations

Thrombotic thrombocytopenic purpura (TTP) is a rare and life-threatening disease. One hallmark is severe ADAMTS13 deficiency, causing ultra-large von Willebrand factor (VWF) multimers to accumulate, leading to microthrombi and lastly to microangiopathic hemolytic anemia and severe thrombocytopenia. Despite great success in recent decades, the molecular picture of the interaction between VWF and ADAMTS13 remains vague. Here, we utilized modern replica-exchange molecular dynamics simulations with the TIGER2h method to sample a vast configurational space of the isolated ADAMTS13-MDTCS domains and the exposure to its substrate and activating cofactor - the unraveled VWF-A2 domain. The sampling of binding sites and conformations was guided and filtered in agreement with available experimental evidence. We provide comprehensive information on exosites for each domain and direct pairs of interacting amino acids, for the first time. The major binding cluster for the active site of the MP domain contrasts the previous mapping of VWF-A2 residues and reciprocal binding pockets. Two major binding modes are revealed and provide access to conformational changes of an extended gatekeeper tetrad upon overcoming local latency during substrate binding and to a dedicated recruitment mechanism. Our work adds the first molecular interaction model that places previous experimental results in perspective to better understand disease-related mutations towards improved therapies. Numerous empirical targets are proposed to verify the given binding modes, to refine the overall picture of MP binding pockets, the role of Dis binding in MP activation and the passage of the Cys-rich domain through VWF-A2, thus deepening the understanding of a highly dynamic interplay.Communicated by Ramaswamy H. Sarma.

Mast Cells in Regeneration of the Skin in Burn Wound with Special Emphasis on Molecular Hydrogen Effect

The mechanisms of regeneration for the fibrous component of the connective tissue of the dermis are still insufficiently studied. The aim of this study was to evaluate the effectiveness of the use of molecular hydrogen on the local therapy of a II degree burn wound with the intensification of collagen fibrillogenesis in the skin. We analyzed the involvement of mast cells (MCs) in the regeneration of the collagen fibers of the connective tissue using water with a high content of molecular hydrogen and in a therapeutic ointment for the cell wounds. Thermal burns led to an increase in the skin MC population, accompanied by a systemic rearrangement of the extracellular matrix. The use of molecular hydrogen for the treatment of burn wounds stimulated the regeneration processes by activating the formation of the fibrous component of the dermis, accelerating wound healing. Thus, the intensification of collagen fibrillogenesis was comparable to the effects of a therapeutic ointment. The remodeling of the extracellular matrix correlated with a decrease in the area of damaged skin. Skin regeneration induced by the activation of the secretory activity of MCs may be one of the possible points of implementation of the biological effects of molecular hydrogen in the treatment of burn wounds. Thus, the positive effects of molecular hydrogen on skin repair can be used in clinical practice to increase the effectiveness of therapy after thermal exposure.

Collagen Type II-Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations

Chitosan-collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence chitosan's affinity for collagen. One of the most important ones is the deacetylation degree (DD) in chitosan and the hydroxylation degree (HD) of proline (PRO) moieties in collagen. In this paper, combinations of both factors were analyzed using a very efficient molecular dynamics approach. It was found that DD and HD modifications significantly affect the structural features of the complex related to considered types of interactions, namely hydrogen bonds, hydrophobic, and ionic contacts. In the case of hydrogen bonds both direct and indirect (water bridges) contacts were examined. In case of the most collagen analogues, a very good correlation between binding free energy and DD was observed.

Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity

Replica exchange molecular dynamics simulations are one of the most popular approaches to enhance conformational sampling of molecular systems. Applications range from protein folding to protein-protein or other host-guest interactions, as well as binding free energy calculations. While these methods are computationally expensive, highly accurate results can be obtained. We recently developed TIGER2hs, an improved version of the temperature intervals with global exchange of replicas (TIGER2) algorithm. This method combines the replica-based enhanced sampling in an explicit solvent with a hybrid solvent energy evaluation. During the exchange attempts, bulk water is replaced by an implicit solvent model, allowing sampling with significantly less replicas than parallel tempering (REMD). This enables accurate enhanced sampling calculations with only a fraction of computational resources compared to REMD. Our latest results highlight several issues with sampling imbalance and parameter sensitivity within the original TIGER2 exchange algorithms that affect the overall state populations. A high sensitivity on replica number and maximum temperature is eliminated by changing to a pairwise exchange kernel (PE) without additional sorting. Simulations are controlled by adjusting the average temperature change per exchange ⟨ΔT/χ⟩ to below 30 K to mimic a controlled temperature mixing of replicas similar to REMD. Thus, this parameter provides an applicable property for selecting combinations of replica number and maximum temperature to adjust simulations for best accuracy, with flexible resource investment. This increases the robustness of the method and ensures results in excellent agreement with REMD, as demonstrated for three different peptides.

Serum collected from rats with myocardial infarction increases extracellular matrix accumulation by myofibroblasts isolated from myocardial infarction scar

The effect on extracellular matrix content is believed to be an average of several serum derived compounds acting in opposition. The aim of the study is to determine whether whole serum of rats with myocardial infarction may modify the accumulation of extracellular matrix in cultures of myofibroblasts isolated from the myocardial infarction scar. A second aim is to determine whether the tested serum can also degranulate the mast cells. Serum was collected from rats with sham myocardial infarction, rats with myocardial infarction induced by coronary artery ligation and control animals. The experiments were carried out on myocardial infarction scar myofibroblasts or mast cells from the peritoneal cavity. The cultures were divided into three groups containing eight cultures each: one treated with serum from control rats, from animals after sham operation or from those after myocardial infarction. In all groups, the serum was used at concentrations of 10%, 20% or 30%. The total collagen content (Woesner method) glycosaminoglycan level (Farandale method), cell proliferation (BrdU), histamine secretion from mast cells (spectrofluorymetry), β1 integrin and α-smooth muscle actin expression (flow cytometry) were evaluated. Isolated cells were α-smooth muscle actin positive and identified as myofibroblasts. Serum derived from rats with myocardial infarction increased collagen and glycosaminoglycan content in the cultures and modified myofibroblast proliferation in a concentration-dependent manner. The serum also results in an imbalance between collagen and glycosaminoglycan levels. The content of β1 integrin was not influenced by myocardial infarction serum. The serum of rats with myocardial infarction is involved in regulation of collagen and glycosaminoglycan content in myofibroblast cultures, as well as the modification of their proliferation. These changes were not accompanied with integrin β1 density variations. The serum of the myocardial infarction rats did not influence the mast cell degranulation.

Two Sides of the Coin: Mast Cells as a Key Regulator of Allergy and Acute/Chronic Inflammation

It is well known that mast cells (MCs) initiate type I allergic reactions and inflammation in a quick response to the various stimulants, including—but not limited to—allergens, pathogen-associated molecular patterns (PAMPs), and damage-associated molecular patterns (DAMPs). MCs highly express receptors of these ligands and proteases (e.g., tryptase, chymase) and cytokines (TNF), and other granular components (e.g., histamine and serotonin) and aggravate the allergic reaction and inflammation. On the other hand, accumulated evidence has revealed that MCs also possess immune-regulatory functions, suppressing chronic inflammation and allergic reactions on some occasions. IL-2 and IL-10 released from MCs inhibit excessive immune responses. Recently, it has been revealed that allergen immunotherapy modulates the function of MCs from their allergic function to their regulatory function to suppress allergic reactions. This evidence suggests the possibility that manipulation of MCs functions will result in a novel approach to the treatment of various MCs-mediated diseases.

Birefringent Silk Fibroin Hydrogel Constructed via Binary Solvent-Exchange-Induced Self-Assembly

Birefringent hydrogels have a strong potential for applications in biomedicine and optics as they can modulate the optical and mechanical anisotropy in confined two-dimensional geometries. However, production of birefringent hydrogels with hierarchical structures, mechanical properties, and biorelated behavior that are analogous to biological tissues is still challenging. Starting from the silk fibroin (SF)-ionic liquid solution system, this study aimed to rationally design a "binary solvent-exchange-induced self-assembly (BSEISA)" strategy to produce birefringent SF hydrogels (SFHs). In this method, the conformational transition rate of SF can be effectively controlled by the exchange rate of the binary solvents. Therefore, this method provides the possibility of controlling the conformation and orientation of SF. Molecular simulations confirmed that methanol is more effective in driving β-sheet formation than other often used solvents, such as formic acid and water. The formed β-sheets act as the physical cross-links that connect disparate protein chains, thereby forming continuous and stable three-dimensional (3D) hydrogel networks. The resultant BSEISA-SFHs are transparent and birefringent with mechanical characteristics similar to those of soft biological tissues, such as lens and cartilage. Interestingly, our results revealed that the evolution of experimental birefringent fringes perfectly matched the changes in stress distribution predicted using finite element analysis. Owing to the unique birefringence of BSEISA-SFHs, together with the advantages in mechanical performance, these hydrogels are anticipated to act as good tissue surrogates for understanding the mechanical response of biological tissues.

Mast cells and collagen fibrillogenesis

This article presents 20 combinations of histochemical stainings for the determination of mast cell co-localization with the fibrous component of the connective tissue in the fibrillogenesis course. Best results were obtained using metachromatic detection of mast cells in combination with silver or picro-fuchsin impregnation, staining with brilliant green using van Gieson staining, and a combination of aniline blue staining with neutral red. Proposed variants of histochemical protocols open up new opportunities to analyze the participation of mast cells in extracellular matrix remodeling of the tissue microenvironment in the course of adaptive and pathological processes. Results obtained expand the current theoretical views of the process of fibrillogenesis in the extracellular matrix. They also shed new light on the participation of mast cell secretion components in the molecular mechanisms of fiber formation.

Molecular dynamics simulations to the bidirectional adhesion signaling pathway of integrin αV β3

The bidirectional force transmission process of integrin through the cell membrane is still not well understood. Several possible mechanisms have been discussed in literature on the basis of experimental data, and in this study, we investigate these mechanisms by free and steered molecular dynamics simulations. For the first time, constant velocity pulling on the complete integrin molecule inside a dipalmitoyl-phosphatidylcholine membrane is conducted. From the results, the most likely mechanism for inside-out and outside-in signaling is the switchblade model with further separation of the transmembrane helices.

Governing the Inhibition of Reconstituted Collagen Type I Assemblies Mediated Through Noncovalent Forces of (±)-α Lipoic Acid

Type I collagen is a fibrous protein, which is highly biocompatible and biodegradable and exhibits low immunogenicity with its unique feature of undergoing a spontaneous self-assembly process. However, the excessive accumulation of collagen may lead to a condition known as fibrosis in vertebrates. Recently, saturated fatty acids have gained much attention as biomedical and therapeutic agents. Therefore, drawing inspiration from the biological and structural tunability of these fatty acids, this work aims to inhibit the self-assembly of type I collagen using (±)-α-lipoic acid (ALA). Reconstituted collagen and its blends with (±)-ALA under physiological conditions were subjected to fibril growth kinetics measurements, which exhibited the decrease in the rate of fibrillogenesis ( t_1/2) with an increase in the concentration of ALA. Variations in the viscoelasticity of collagen and ALA blend with respect to rate and frequency showed significant changes. Further, the frequency shifts of different functional groups via FT-IR (ATR) and the morphological changes associated with fibril inhibition were visualized using a cryoscanning electron microscope. Molecular dynamics simulation of the collagen-like peptide with the (±)-ALA molecule at different molar ratios proved that (±)-ALA had a strong potential to bind at various sites of collagen mediated by conventional secondary or noncovalent forces. Thus, the protein-small molecule interaction dominates the forces prevailing between protein-protein binding, leading to the inhibition of the self-assembly process. Such inhibitory effects by a fatty acid may unfold newer avenues for development of targeted and sustainable drug delivery systems for fibrotic diseases.

Replica-Based Protein Structure Sampling Methods: Compromising between Explicit and Implicit Solvents

The structure of a protein is often not completely accessible by experiments. In silico, replica exchange molecular dynamics (REMD) is the standard sampling method for predicting the secondary and tertiary structures from the amino acid sequence, but it is computationally very expensive. Two recent adaptations from REMD, temperature intervals with global exchange of replicas (TIGER2) and TIGER2A, have been tested here in implicit and explicit solvents. Additionally, explicit, implicit, and hybrid solvent REMD are compared. On the basis of the hybrid REMD (REMDh) method, we present a new hybrid TIGER2h algorithm for faster structural sampling, while retaining good accuracy. The implementations of REMDh, TIGER2, TIGER2A, and TIGER2h are provided for nanoscale molecular dynamics (NAMD). All the methods were tested with two model peptides of known structure, (AAQAA)₃ and HP7, with helix and sheet motifs, respectively. The TIGER2 methods and REMDh were also applied to the unknown structure of the collagen type I telopeptides, which represent bigger proteins with some degree of disorder. We present simulations covering more than 180 μs and analyze the performance and convergence of the distributions of states between the particular methods by dihedral principal component and secondary structure analysis.

Multiscale modeling of glycosaminoglycan structure and dynamics: current methods and challenges

Glycosaminoglycans are long unbranched and complex polysaccharides that are an essential component of mammalian extracellular matrices. Characterization of their molecular structure, dynamics and interactions are essential to understand important biological phenomena in health and disease, and will lead to novel therapeutics and medical devices. However, this has proven to be a challenge experimentally and theoretical techniques are needed to develop new hypotheses, and interpret experiments. This review aims to examine the current theoretical (rather than experimental) methods used by researchers to investigate glycosaminoglycan structure, dynamics and interactions, from the monosaccharide to the macromolecular scale. It will consider techniques such as quantum mechanics, molecular mechanics, molecular dynamics, coarse graining and docking.