Molecular Nanoscale Research Articles

Implementation of magnetic field force in molecular dynamics algorithm: NAMD source code version 2.12.

The external fields, such as the magnetic force, have made advances in many industrial and biotechnology applications during the past century, although the changes in the structure of materials under the impact of the electromagnetic fields have not entirely been clear yet. The molecular simulation technique by providing extensive data from the configuration and orientations of the atoms is becoming the effective useful tool for scientists in a wide range of research areas. This paper presents an extended velocity Verlet algorithm inside the Nanoscale Molecular Dynamics (NAMD) package that enhances the NAMD features with the capability to compute the magnetic field force. We described how this novel feature has been implemented inside the package. Moreover, the results are reported for the rotation of a charged particle, and the thermo-physical properties of water in the presence of a magnetic field confirming how this developed NAMD source code provides accurate measurements compared with other available data.

Comparison of CHARMM and OPLS-aa forcefield predictions for components in one model asphalt mixture

Molecular dynamics simulations have been widely applied to understand the effect of chemical composition on the major physical and mechanical properties and micro-structure of asphalt. However, the choice of forcefields has been mostly empirical. In this project, two commonly used forcefields, the Chemistry at Harvard Macromolecular Mechanics (CHARMM) forcefield and the Optimized Potentials for Liquid Simulations in all atom version (OPLS-aa) forcefield were evaluated, side by side for simulation of the three main components of one model asphalt mixture to compare the effectiveness of the forcefields. The CHARMM forcefield parameters for two smaller components —including n-docosane and 1,7-dimethylnaphthalene molecules—were obtained using the CGENFF program; the forcefield parameters for an average asphaltene molecule were obtained with the VMD forcefield toolkit and Gaussian quantum calculations. Comparing molecule structures of asphaltene, 1,7-dimethylnaphthalene and n-docosane (n-C22) predicted using the CHARMM forcefield to those from traditional OPLS-aa forcefield, the energy-minimized structures are very similar. At a high temperature such as 300 K and above, slight bending on the aromatic ring regions and the alkane chains was observed for the asphaltene molecule; kinking of the n-docosane molecule chain structure was also observed using both forcefields; and the structure of 1,7-dimethylnaphthalene is consistent at both low and high temperatures. Comparing the properties predicted based on the long-term simulation trajectories, the density, diffusion coefficient and g(r) result of asphaltene, 1,7-dimethylnaphthalene and n-docosane from the CHARMM and Nanoscale Molecular Dynamics (NAMD) program are very close to those from the OPLS-aa forcefield and LAMMPS program. However, the CHARMM forcefield correctly predicted the crystallization of n-docosane at 300 K while the OPLS-aa forcefield did not.

Prediction of binding characteristics between von Willebrand factor and platelet glycoprotein Ibα with various mutations by molecular dynamic simulation

IntroductionBinding of platelet glycoprotein (GP)Ibα with von-Willebrand factor (VWF) exclusively mediates the initial platelet adhesion to injured vessel wall. To understand the mechanism of biomedical functions, we calculated the dynamic fluctuating three-dimensional (3D) structures and dissociation energy for GPIbα with various single amino-acid substitution at G233, which location is known to cause significant changes in platelet adhesive characteristics. Material and methodsMolecular dynamics (MD) simulation was utilized to calculate 3D structures and Potential of Mean Force (PMF) for wild-type VWF bound with wild-type, G233A (equal function), G233V (gain of function), and G233D (loss of function) GPIbα. Simulation was done on water-soluble condition with time-step of 2 × 10−15 s using NAnoscale Molecular Dynamics (NAMD) with Chemistry at HARvard Molecular Mechanics (CHARMM) force field. Initial structure for each mutant was obtained by inducing single amino-acid substitution to the stable water-soluble binding structure of wild-type. ResultsThe most stable structures of wild-type VWF bound to GPIbα in wild-type or any mutant did not differ. However, bond dissociation energy defined as difference of PMF between most stable structure and the structure at 65 Å mass center distances in G233D was 4.32 kcal/mol (19.5%) lower than that of wild-type. Approximately, 2.07 kcal/mol energy was required to dissociate VWF from GPIbα with G233V at mass center distance from 48 to 52 Å, which may explain the apparent “gain of function” in G233V. ConclusionThe mechanism of substantially different biochemical characteristics of GPIbα with mutations in G233 location was predicted from physical movement of atoms constructing these proteins.

Nanoscale Molecular Fractionation of Organic Matter within Unconventional Petroleum Source Beds

Fractionation of petroleum during migration through sedimentary rock matrices has been observed across lengths of meters to kilometers. Selective adsorption of specific chemical moieties at mineral...

High Throughput Virtual Screening and Mutational Studies Using Docking and Molecular Dynamics on a Shared Memory GPU Supercomputer

Human Fructose 1,6 Bisphosphatase (FBPase), an enzyme which serves as the control point in the gluconeogenesis pathway, was selected as a protein target for this study. FBPase is a putative target for drug development to combat Type II Diabetes. The FBPase protein structure has previously been solved (Zhang et al., 1995), and coordinates were readily available (PDB code IFTA) and downloaded for docking studies from the Rutgers Consortium of Structural Biology (RCSB) Protein Data Bank (PDB). The potential inhibitory molecules (IBS Natural Products Catalog) were downloaded from the ZINC Database (Irwin et al., 2012) in pdbqt file format. AutoDock Vina was selected as the ideal docking program for FBPase as determined by comparing co‐crystallized ligands to docked ligand positions. Selected compounds were chosen and docked into the FBPase active site and allosteric binding sites. Following the identification of promising theoretical binding constants for each molecule, molecular dynamics studies were performed for the FBPase protein target in the absence and presence of these promising molecules. Studies were caeried out using a NAMD/VMD (Nanoscale Molecular Dynamics with Visual Molecular Dynamics) system. NAMD implemented with CHARMM foce field is known to be highly efficient in simulating large systems for molecular motions. Dissociation constants (Ki) for the protein‐ligand complexes were calculated through NAMD runs, and respective conformational changes in the FBPase binding pockets were observed. Binding pockets were evaluated based on two factors: 1) pocket shape, and 2) pocket volume. Laboratory‐based site‐directed mutagenesis results revealed various levels of activation/inhibition of the enzyme as a result of mutations, an outcome with genetic implications for disease. Mutant enzymes resisted attempts at crystallization so molecular dynamics (MD) studies were performed on models of mutants. Focused on the active site of allosteric binding sites, further analysis was performed with key residues (virtually mutated) to initiate activation or inhibition of the enzyme (retention in T‐state or transition to R‐state) using NAMD. Resulting models of FBPase after MD runs shed light on possible interfacial structural changes produced in response to these mutations. Structural alterations in the models were observed in the active site, AMP (adenosine monophosphate) allosteric binding site, dimer interface allosteric binding site, and the interface between the active site and the AMP binding site. The signal from one part of the molecule is trasmittedto another part of the molecule through a known hydrogen‐bonding network (a sequential allosteric transition) vconnecting the active sites to the AMP allosteric binding sites. Novel hydrophobic networks were identified to connect the active sites to the allosteric binding sites using the NAMD protocol.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Immunoinformatics Approach to Design T-cell Epitope-Based Vaccine Against Hendra Virus

Screening of HLA class II epitope-based peptides as potential vaccine candidates is one of the most rational approach for vaccine development against Hendra virus (HeV) infection, for which currently there is no successful vaccine in practice. In this study, screening of epitopes from HeV proteins viz matrix, glycoprotein, nucleocapsid, fusion, C protein, V protein, W protein and polymerase, followed by highest binding affinity & molecular dynamic simulation of selected T-cell epitopes with their corresponding HLA class II alleles has been done. The server ProPred facilitates the binding prediction of HLA class II allele specific epitopes from the antigenic protein sequences of HeV. PEPstrMOD server was used for PDB structure modeling of the screened epitopes and MODELLER was used for HLA alleles modeling. We docked the selected T-cell epitopes with their corresponding HLA allele structures using the AutoDock 4.2 tool. Further the selected docked complex structures were optimized by NAnoscale Molecular Dynamics program (NAMD) at 5 ps, with the CHARMM-22 force field parameter incorporated in Visual Molecular Dynamics (VMD 1.9.2) and complex structure stability was evaluated by calculating RMSD values. Epitopes IRIFVPATN (Nucleocapsid), MRNLLSQSL (Nucleocapsid), VRRAGKYYS (Matrix) and VRLKCLLCG (Fusion) proteins have shown considerable binding with DRB1*0806, DRB1*1304, DRB1*0701 and DRB1*0301 HLA class II allele respectively. Toxicity, antigenicity and population coverage of epitopes IRIFVPATN, MRNLLSQSL, VRRAGKYYS and VRLKCLLCG were analyzed by Toxin Pred, Vexijen and IEDB tool, respectively. The potential T-cell epitopes can be utilized in designing comprehensive epitope-based vaccines and diagnostic kits against Hendra virus after further in-vivo studies.

Stability of β-turn in LaR2C-N7 peptide for its translation-inhibitory activity against hepatitis C viral infection: A molecular dynamics study.

Hepatitis C virus (HCV) requires an essential host factor, human La protein, for its translation and replication activity. Earlier, it was demonstrated that a 24-mer synthetic peptide (LaR2C) encompassing residues 112 to 184 of the natural human La protein interacts with the HCV internal ribosome entry site (IRES) and inhibits translation. Interestingly, a shorter version of the same LaR2C peptide, LaR2C-N7, containing residues 174 to 180 (KYKETDL), with a unique β-turn secondary structure, is sufficient to inhibit IRES mediated translation of HCV. Hence, it is imperative to understand the role of each amino acid of this heptapeptide towards β-turn formation which will then help in designing potential drugs against HCV infection. Here, we use Nanoscale Molecular Dynamics (NAMD) simulation to investigate the factors modulating its β-turn formation and stability. Using 100 ns simulation paradigms, we find that the peptide populated the type 1 β-turn conformation in its free form in solution. However, simulation of the single-site mutants of the heptapeptide revealed that none of the 7 mutants retained the β-turn conformation with sufficient stability. We observed that the β-turn was stabilized mainly by the side chain interaction, salt-bridge and weak hydrogen bonds between K3 and D6 residues. Y2, K1 and K3 sites upon mutation heavily destabilized the β-turn when compared to alteration at the E4 and T5 sites which would then drastically reduce its HCV RNA IRES binding capabilities. Taken together, our results provide a basis for designing peptidomimetics as potential anti-HCV drug candidates.

Scalable Molecular Dynamics with NAMD on the Summit System.

NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and dynamics of large biomolecular complexes, such as viruses like HIV and various types of influenza. State-of-the-art biomolecular simulations often require integration of billions of timesteps, computing all interatomic forces for each femtosecond timestep. Molecular dynamics simulation of large biomolecular systems and long-timescale biological phenomena requires tremendous computing power. NAMD harnesses the power of thousands of heterogeneous processors to meet this demand. In this paper, we present algorithm improvements and performance optimizations that enable NAMD to achieve high performance on the IBM Newell platform (with POWER9 processors and NVIDIA Volta V100 GPUs) which underpins the Oak Ridge National Laboratory's Summit and Lawrence Livermore National Laboratory's Sierra supercomputers. The Top-500 supercomputers June 2018 list shows Summit at the number one spot with 187 Petaflop/s peak performance and Sierra third with 119 Petaflop/s. Optimizations for NAMD on Summit include: data layout changes for GPU acceleration and CPU vectorization, improving GPU offload efficiency, increasing performance with PAMI support in Charm++, improving efficiency of FFT calculations, improving load balancing, enabling better CPU vectorization and cache performance, and providing an alternative thermostat through stochastic velocity rescaling. We also present performance scaling results on early Newell systems.

Near-Field Spectroscopy of Nanoscale Molecular Aggregates.

When molecules are assembled into an aggregate, their mutual dipole-dipole interaction leads to electronic eigenstates that are coherently delocalized over many molecules. Knowledge about these states is important to understand the optical and transfer properties of the aggregates. Optical spectroscopy, in principle, allows one to infer information on these eigenstates and about the interactions between the molecules. However, traditional optical techniques using an electromagnetic field which is uniform over the relevant size of the aggregate cannot access most of the excited states because of selection rules. We demonstrate that by using localized fields one can obtain information about these otherwise inaccessible states. As an example, we discuss in detail the case of local excitation via radiation from the apex of a metallic tip, which allows also scanning across the aggregate. The resulting spatially resolved spectra provide extensive information on the eigenenergies and wave functions. Finally we show that the technique will elucidate the anomalous temperature dependence of superradiance found recently for two-dimensional aggregates of the semiconductor PTCDA formed on a KCl surface.

Impact of Contact in Molecular Junctions: When Physics Dictates the Chemical Properties

Molecular junctions are nanomaterials made of one molecule, or a thin organic layer, sandwiched between two metallic electrodes.[1] These systems are now widely and intensively studied due to a high potential for nanoelectronic applications. If these devices can now be reliably made and characterized, this field of research is facing a clear issue: the modification of the molecular structure offers a poor control over the device characteristics. The basic idea of the design in Molecular Electronics is that the molecular level landscape in the junction will affect the electron transport, offering control over the current/voltage characteristics.[1-3] Driven by chemical intuition, the usual design of molecular junctions relies on electron donating or accepting building blocks. In this presentation, we show and explain that this approach which focuses on the isolated molecule properties provides a very limited or even erroneous picture as the contact of a molecule to two metal electrodes leads to a completely different entity. Using first principle DFT calculations, we demonstrate that the contact of an asymmetric organic layer to metal electrodes comes with the creation of spontaneous and very intense electric fields in the junction.[4] The origin of this field are the permanent dipole moments in the junction. The built-in field completely modifies the energy landscape in the junction. We argue that only a design that takes into account such large contact renormalization effects could finally lead to the control of the electronic structure of molecular junctions and then move the molecular electronics effort in the intelligent design era. [1] Aviram and Ratner, Chemical Physics Letters, “Molecular rectifiers”, 1974 [2] Van Dyck and Ratner, Nano Letters, 10.1021/nl504091v, 2015 [3] Van Dyck and Ratner, J. Phys. Chem. C, 10.1021/acs.jpcc.6b07855, 2017 [4] Van Dyck and Bergren, Accepted in Advanced Electronic Materials, “Large Built-in Fields Control the Electronic Properties of Nanoscale Molecular Devices with Dipolar Structures”, 2018 Figure 1

Evolution of HJ Coupling in Nanoscale Molecular Self-Assemblies

We investigated the evolution of combined Frenkel exciton and charge-transfer chromophore coupling in nanoscale self-assembled clusters of 7,8,15,16-tetraazaterrylene. Using spatially and wavelength-resolved fluorescence imaging, we observed significant changes in the relative intensities of vibronic transitions (J-like to H-like) in isolated clusters with increasing size (along the crystal growth axis), suggestive of a change in the interference of the combined short- and long-range interactions upon assembly. Large clusters and nanowires showed spectral signatures that appear superficially like H-aggregates with a diminished origin (0–0) intensity relative to the higher vibronic sidebands, whereas small nanoclusters—appearing as diffraction limited spots—had distinct J-aggregate spectral signatures (enhancement of the origin intensity) suggestive of different packing structures in small clusters. The isolation of the different nanoscale assemblies allows for the opportunity to understand changes in mole...

Large Built‐In Fields Control the Electronic Properties of Nanoscale Molecular Devices with Dipolar Structures

AbstractLarge area molecular junctions are nanoscale materials made of a molecular layer sandwiched between two metal electrodes. In this study, a fundamental property of these systems is demonstrated: the emergence of a large built‐in field, typically as high as 109 V m−1, and susceptible to appear in any junction possessing an asymmetry. This field originates from permanent dipoles in the contacted molecular layer and is responsible for a large renormalization of the band alignment in the junction. To illustrate this effect, a predictive theoretical characterization of two realistic gold‐thiolate‐based organic layers is carried out. The parameters leading to the emergence of the built‐in field are given and the very large renormalization effect is interpreted in terms of an applied voltage drop. Despite a high significance, this generic feature of molecular junctions has widely been neglected hitherto in the design and interpretation of molecular device characteristics. Built‐in fields provide a powerful way to achieve structure–property relationships in molecular junctions, by taking advantage of dipolar nanometric building blocks.

Cover Feature: Copper(I)–Dioxygen Reactivity in the Isolated Cavity of a Nanoscale Molecular Architecture (Eur. J. Inorg. Chem. 19/2018)

Cover Feature: Copper(I)–Dioxygen Reactivity in the Isolated Cavity of a Nanoscale Molecular Architecture (Eur. J. Inorg. Chem. 19/2018)

Copper(I)–Dioxygen Reactivity in the Isolated Cavity of a Nanoscale Molecular Architecture

Copper(I) and copper(II) complexes supported by a bulky tetradentate N4 ligand, [CuI(TIPT3tren)(CH3CN)]ClO4 (1) and [CuII(TIPT3tren)Cl]BF4 (2), were synthesized and characterized, where TIPT is 2,2′′,6,6′′‐tetraisopropyl‐1,3′:5′,1′′‐terphenyl and tren is tris(2‐aminoethyl)amine. The copper(II) chloride complex 2 exhibits a trigonal‐bipyramidal structure, as usually observed for the tren ligand system, in which the chloride ligand occupies an axial position and is encapsulated in an isolated cavity consisting of three TIPT substituents. Such a trigonal‐bipyramidal structure is stabilized in acetone, in which hydrogen‐bonding interactions between the anilino N–H groups and the oxygen atom of the acetone molecules, entrapped in the hydrophobic clefts between the TIPT substituents, play an important role. The reaction of copper(I) complex 1 and O2 in an acetone‐containing solvent at –110 °C gave end‐on copper(II) superoxide complex 3 together with putative side‐on copper(III) peroxide complex 4, as was evident from detailed studies by variable‐temperature UV/Vis, resonance Raman, and 1H and 2H NMR spectroscopy. The formation of 3 and 4 was also validated by DFT calculations.

Molecular dynamics investigation of surfactant micelles as a potential drug delivery vehicle

A new molecular dynamics study is being initiated in which micellar structures of cetyltrimethylammonium bromide (CTAB) are simulated within computationally constructed physiological conditions. Leading up to the simulation phase, several programs and reference files were used to construct a topology file, initial structure/coordinate files, and parameter files to accurately represent a single molecule of CTAB. This single molecule is utilized in making the initial configuration of a system. All systems begin in one of three configurations: a random assembly of molecules in a box, a pre-formed micelle, or an inverse micelle. These initial configurations, once assembled, are placed under generated physiological conditions by using Visual Molecular Dynamics (VMD) to solvate the system with water and add Na+ and Cl- ions to neutralize the system to 0.15 M NaCl, then using Nanoscale Molecular Dynamics (NAMD) to minimize energy and heat the system to 310 K. The system is then simulated using NAMD until a micelle has formed and stabilized. Following each simulation, quantitative and qualitative analysis is used to characterize the system. The overarching goal of this study is to determine the viability of CTAB as a drug carrier in a targeted drug delivery system. Funding for the project is provided by the College of Science and Technology at Fairmont State University and the NASA WV Space Grant Consortium.

Nanoscale Molecular Dynamics Simulation and Free Energy Decomposition of Hepatitis C Virus and its Interaction with GTP

Hepatitis C Virus (HCV) NS5B protein is a RNA-dependent RNA polymerase essential for replication of the viral RNA genome. Genome of HCV is an RNA molecule of approximately 9600 nucleotides, structured in a coding region that contains one large open reading frame (ORF), flanked by non-translated regions (NTR) at the 5’ and 3’ ends encoding a polyprotein precursor of about 3,000 amino acids. High concentrations of GTP (guanosine 5’-triphosphate) have been shown to stimulate de novo RNA synthesis by HCV NS5B. Molecular dynamics (MD) simulations have been performed on NS5B complex to investigate the stability and conformational changes with GTP. It is observed that the backbone atom of NS5B attains stability after 50ns. In vitro, NS5B has been shown to be capable of template-directed RNA synthesis on its own, requiring only divalent metals (magnesium or manganese) as cofactors. In addition, the MM-GBSA approach was introduced to analyze the interactions between inhibitors and NS5B.

Increasing vaccine production using pulsed ultrasound waves.

Vaccination is a safe and effective approach to prevent deadly diseases. To increase vaccine production, we propose that a mechanical stimulation can enhance protein production. In order to prove this hypothesis, Sf9 insect cells were used to evaluate the increase in the expression of a fusion protein from hepatitis B virus (HBV S1/S2). We discovered that the ultrasound stimulation at a frequency of 1.5 MHz, intensity of 60 mW/cm2, for a duration of 10 minutes per day increased HBV S1/S2 by 27%. We further derived a model for transport through a cell membrane under the effect of ultrasound waves, tested the key assumptions of the model through a molecular dynamics simulation package, NAMD (Nanoscale Molecular Dynamics program) and utilized CHARMM force field in a steered molecular dynamics environment. The results show that ultrasound waves can increase cell permeability, which, in turn, can enhance nutrient / waste exchange thus leading to enhanced vaccine production. This finding is very meaningful in either shortening vaccine production time, or increasing the yield of proteins for use as vaccines.

A QSAR model of Olanzapine derivatives as potential inhibitors for 5-HT2A Receptor.

Schizophrenia is a complex, chronic mental disorder, affecting about 21 million people worldwide. It is characterized by symptoms, including distortions in thinking, perception, emotions, disorganized speech, sense of self and behavior. Recently, a numbers of marketed drugs for Schizophrenia are available against dopamine D2 and serotonin 5-HT2A receptors. Here, we docked Olanzapine derivatives (collected from literature) with 5-HT2A Receptor using the program AutoDock 4.2. The docked protein inhibitor complex structure was optimized using molecular dynamics simulation for 5ps with the CHARMM-22 force field using NAMD (NAnoscale Molecular Dynamics program) incorporated in visual molecular dynamics (VMD 1.9.2) and then evaluating the stability of complex structure by calculating RMSD values. NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. A quantitative structure activity relationship (QSAR) model was built using energy-based descriptors as independent variable and pKi value as dependent variable of eleven known Olanzapine derivatives with 5-HT2A Receptor, yielding correlation coefficient r2 of 0.63861. The predictive performance of QSAR model was assessed using different crossvalidation procedures. Our results suggest that a ligand-receptor binding interaction for 5-HT2A receptor using a QSAR model is promising approach to design more potent 5-HT2A receptor inhibitors prior to their synthesis.

Structural and functional characterization of the divergent Entamoeba Src using Src inhibitor-1

BackgroundThe abundant number of kinases that Entamoeba histolytica possesses allows us to assume that the regulation of cellular functions by phosphorylation-dephosphorylation processes is very important. However, the kinases responsible for the phosphorylation in Entamoeba spp. vary in the structure of their domains and, therefore, could be responsible for the unusual biological characteristics of this parasite. In higher eukaryotes, Src kinases share conserved structural domains and are very important in the regulation of the actin cytoskeleton. In both Entamoeba histolytica and Entamoeba invadens, the major Src kinase homologue of higher eukaryotes lacks SH3 and SH2 domains, but does have KELCH domains; the latter are part of actin cross-linking proteins in higher eukaryotic cells.MethodsThe function of the EhSrc protein kinase of Entamoeba spp. was evaluated using Src inhibitor-1, microscopy assays, Src kinase activity and western blot. In addition, to define the potential inhibitory mechanism of Src-inhibitor-1 for the amoebic EhSrc protein kinase, molecular dynamic simulations using NAnoscale Molecular Dynamics (NAMD2) program and docking studies were performed with MOE software.ResultsWe demonstrate that Src inhibitor-1 is able to prevent the activity of EhSrc protein kinase, most likely by binding to the catalytic domain, which affects cell morphology via the disruption of actin cytoskeleton remodeling and the formation of phagocytic structures without an effect on cell adhesion. Furthermore, in E. invadens, Src inhibitor-1 inhibited the encystment process by blocking RhoA GTPase activity, a small GTPase protein of Rho family.ConclusionsEven though the EhSrc molecule of Entamoeba is not a typical Src, because its divergent amino acid sequence, it is a critical factor in the biology of this parasite via the regulation of actin cytoskeleton remodeling via RhoA GTPase activation. Based on this, we conclude that EhSrc could become a target molecule for the future design of drugs that can prevent the transmission of the disease.

The Secret Life of Collagen: Temporal Changes in Nanoscale Fibrillar Pre-Strain and Molecular Organization during Physiological Loading of Cartilage.

Articular cartilage is a natural biomaterial whose structure at the micro- and nanoscale is critical for healthy joint function and where degeneration is associated with widespread disorders such as osteoarthritis. At the nanoscale, cartilage mechanical functionality is dependent on the collagen fibrils and hydrated proteoglycans that form the extracellular matrix. The dynamic response of these ultrastructural building blocks at the nanoscale, however, remains unclear. Here we measure time-resolved changes in collagen fibril strain, using small-angle X-ray diffraction during compression of bovine and human cartilage explants. We demonstrate the existence of a collagen fibril tensile pre-strain, estimated from the D-period at approximately 1-2%, due to osmotic swelling pressure from the proteoglycan. We reveal a rapid reduction and recovery of this pre-strain which occurs during stress relaxation, approximately 60 s after the onset of peak load. Furthermore, we show that this reduction in pre-strain is linked to disordering in the intrafibrillar molecular packing, alongside changes in the axial overlapping of tropocollagen molecules within the fibril. Tissue degradation in the form of selective proteoglycan removal disrupts both the collagen fibril pre-strain and the transient response during stress relaxation. This study bridges a fundamental gap in the knowledge describing time-dependent changes in collagen pre-strain and molecular organization that occur during physiological loading of articular cartilage. The ultrastructural details of this transient response are likely to transform our understanding of the role of collagen fibril nanomechanics in the biomechanics of cartilage and other hydrated soft tissues.