Biology subjects

Harms, C.

Publications and source records attributed to Harms, C..

16 recordsLinked to original sources

bioRxiv2026

Drug design using unique conformations to preferentially target a specific site on collagen-bound MMP1

Precise site-specific drug design remains a challenge in structure-based drug discovery. Most existing approaches screen for ligands to target binding pockets on a protein surface based on static structures obtained from techniques such as X-ray, NMR, cryo-EM, and AlphaFold. However, the structure-function paradigm is, in reality, a structure-dynamics-function relationship that determines a proteins binding and activity. As such, drug screening or design without evaluating binding competition across the protein surface or considering the receptors dynamic, substrate-dependent conformational states is incomplete. Substrate-specific unique protein conformations are underexplored and offer novel opportunities for selective therapeutic targeting, though systematic workflows for identifying and exploiting such sites remain limited. Previously, we showed that collagen alters matrix metalloprotease-1 (MMP1) dynamics and that R405 is an allosteric residue on the MMP1 surface that exhibits strong dynamic correlations with its active site. Here, we present a substrate-specific allosteric drug-design framework that targets specific sites on a protein, using collagen-bound MMP1 as a model system. We determined the conformational dynamics of free and collagen-bound MMP1 using all-atom molecular dynamics (MD) simulations and categorized conformations into clusters of similar conformations. We then compared and identified unique conformations that occur only in collagen-bound MMP1 to design drugs against them using a machine-learning approach. The top three unique clusters were used to generate approximately 150,000 candidate compounds that were then screened against both the R405-centered region and all detectable binding pockets across the MMP1 surface. We have found several compounds that bind preferentially around R405 by at least 0.3 kcal/mol relative to competing sites across the surface. This strategy establishes a generalizable framework for designing ligands that preferentially target substrate-specific allosteric sites, providing new opportunities for precision therapeutics that modulate proteins in their biologically relevant functional states. Simple SummaryIn this paper, we establish a substrate-specific allosteric drug-design strategy that integrates all-atom molecular dynamics simulations, conformational clustering, machine-learning-based ligand design, and surface-wide binding-selectivity screening, using collagen-bound MMP1 as a model system. We show that collagen binding reshapes the conformational ensemble of MMP1, creating unique conformational states that are absent or inaccessible in the free enzyme. By identifying these substrate-specific conformations, generating ligands based on the corresponding dynamic fingerprints around the collagen-specific allosteric residue R405, and screening compounds across all binding pockets on the MMP1 surface, we demonstrate preferential targeting of the collagen-specific site relative to competing pockets. These results establish a generalizable framework for designing ligands that selectively recognize biologically relevant substrate-bound conformations rather than static protein structures alone. Substrate-specific allosteric targeting may enable selective modulation of individual protein functions while minimizing off-target interactions, providing new opportunities for precision therapeutics against dynamic protein systems.

biophysics↗

bioRxiv2025

Change in motor state equilibrium explains prokinetic effect of apomorphine on locomotion in experimental Parkinsonism

Gait impairments remain a major therapeutic challenge in Parkinsons disease (PD). Apomorphine is gaining renewed clinical attention with the expanding use of pump infusion systems. Yet, the specific role of apomorphine on the neural regulation of gait has remained poorly characterized, limiting its targeted use for symptom-specific therapy in PD. Here, we examined the neurobehavioral effects of apomorphine on runway locomotion in the unilateral 6-hydroxydopamine (6-OHDA) rat model. Therapeutic drug doses significantly increased total walking distance, related to reduced akinesia and prolonged gait episodes. Conversely, 3D kinematic analysis revealed reduced limb velocities under medication. At the neural level, therapy doses selectively enhanced cortical high-gamma rhythms without substantially altering beta or low-gamma activity. Instead, beta and low-gamma oscillations were consistently suppressed during motor activity in both medication ON and OFF conditions. Neurobehavioral correlations showed that transitions into gait were facilitated by reductions in beta and low-gamma activity, whereas transitions to akinesia were primarily suppressed when high-gamma activity was elevated. Our findings suggest that modulating cortical activity can aid ameliorating gait deficits in PD. We further propose that the complex therapy effects of apomorphine are best explained by a shift in motor-state equilibrium that is defined by the transitions of akinesia, stationary movements and gait. Together, these insights establish a mechanistic framework to guide the development of targeted gait therapies in PD.

neuroscience↗

bioRxiv2025

Uncovering the Neural Fingerprint of Akinetic States in a Parkinsons Disease Rodent Model

Gait deficits present an unresolved therapeutic challenge in Parkinsons Disease. At the behavioral level, symptoms exhibit heterogeneity, including bradykinesia and hypokinesia during cyclical limb movement, as well as sudden interruptions in the gait sequence, also known as freezing of gait. The neural activities that drive these various deficits remain largely unknown. Here, we investigated the neural correlates of gait sequence interruptions with deep neurobehavioral phenotyping. For this, we transformed kinematic trajectories and cortical oscillations into continuous time series of multimodal feature vectors. Next, we applied machine learning, combining low-dimensional embedding with supervised classification, to identify cortical oscillation features that drive gait deficits. In a rodent Parkinsons disease model, our approach revealed that gait, akinesia, and stationary movements occupy prominently different regions in the low-dimensional embedding space. Among the predominant features separating the states, we found Hjorth complexity and mobility to modulate with the onset of akinetic episodes. Additionally, we validated our analysis approach in two Parkinson patients with freezing of gait, where neural features in STN recordings partially reflected the findings from ECoG measurements in rodents. The presented neurobehavioral phenotyping approach is translational and can easily generalize to the analysis of other complex movement disorders. Together, our results highlight specific features of neural oscillations as potential biomarkers that may support the development of adaptive closed-loop algorithms for gait therapy in PD.

neuroscience↗

bioRxiv2025

The substrate changes matrix metalloprotease-1 dynamics, allostery, and ligand binding affinity

Using single-molecule experiments, ensemble assays, and Molecular Dynamics (MD) simulations, we showed that collagen actively influences MMP1 interdomain dynamics. This paper extends the previous experimental work to validate MD simulations and gain more insights into MMP1-collagen interactions. We include virtual screening with free energy calculations to uncover key insights regarding substrate-dependent dynamics, allostery, and ligand binding. Our findings reveal that MMP1 interdomain dynamics are influenced by the strain in collagen, and collagen-specific allosteric residues exhibit strong correlations with the active site. Additionally, allosteric paths connecting these residues to the active site bypass the linker region. Collagen also induces changes in the configurations of the catalytic motif. Furthermore, MD simulation and virtual screening identify molecules that bind to allosteric residues, alter MMP1 dynamics, and potentially change activity. Free energy calculations highlight the essential role of the substrate in small molecule screening against a protein. We have developed a comprehensive framework for identifying substrate-specific allosteric residues in MMP1 and screening small molecules incorporating protein dynamics in the presence of substrates. These results significantly impact our understanding of MMP1 interactions with collagen fibrils and pave the way for selectively modulating specific MMP1 functions without altering its other functions in future applications. SignificanceIn this paper, we validated all-atom simulations of free and collagen-bound MMP1 and gained insights into MMP1 function. We have found that collagen changes dynamics, allostery, and ligand binding in MMP1. Collagen strain, known to be age-dependent, also changes MMP1 dynamics and ligand binding. Interdomain allosteric paths do not go through the linker connecting the MMP1 domains. Instead, paths from the collagen-specific allosteric residue to the active site have non-bonded interactions. Screening of small molecules against collagen-specific MMP1 residue suggests that collagen alters ligand binding to MMP1. These results will significantly impact understanding MMPs and small molecule screening against proteins. Substrate-specific allosteric residues may enable controlling one function of MMPs without altering their other functions, leading to fewer side effects.

biophysics↗

bioRxiv2024

Capture and Release of Minke Whales Offers New Research Opportunities Including Measurements of Mysticete Hearing

Knowledge about species-specific hearing is vital to assessing how anthropogenic noise impacts marine mammals. Unfortunately, no empirical audiogram exists for any mysticete whale. We therefore developed a catch-and-release method to assess hearing in a small mysticete, the minke whale (Balaenoptera acutorostrata). Stationary lead nets were placed to intercept migratory routes and direct animals into an ocean basin enclosed by nets and islets, while another net was pulled across the entrance once a whale entered the basin. The whales were then slowly corralled into a modified aquaculture pen using a net suspended between two boats. Subsequently, the water volume available to the whales was gradually reduced by raising the pen net by hand until the whales were secured in a "hammock" between the floating pen ring and a raft. From the raft, researchers could access the whales to monitor their health, apply instruments for hearing tests, or other research objectives, and attach tags to monitor the movements and diving behavior of the whale post-release. The method is a slow and controlled procedure, allowing continuous monitoring, and quick release of the whales, if needed. In the first three field seasons employing the method, three animals were caught for research procedures. Initial hearing measurements using auditory evoked potentials were successfully completed. After release the animals resumed migration and dive behavior were considered normal. Our observations demonstrate that minke whales can be safely guided via moored net barriers, corralled into an aquaculture pen, and safely handled for research purposes, before being released back into the wild.

physiology↗

bioRxiv2023

Refined movement analysis in the Staircase test reveals differential motor deficits in mouse models of stroke

Accurate assessment of post-stroke deficits is vital in translational research. Recent advances in machine learning provide unprecedented precision in quantifying rodent motor behavior post-stroke. However, the extent to which these tools can detect lesion-specific upper extremity deficits remains unclear. Using proximal middle cerebral artery occlusion (MCAO) and cortical photothrombosis (PT), we assessed post-stroke impairments in mice through the Staircase test. Lesion locations were identified using 7T-MRI. Machine learning was applied to reconstruct kinematic trajectories using MouseReach, a data-processing toolbox. This yielded 30 refined outcome parameters effectively capturing motor deficits. Lesion reconstructions located ischemic centers in the striatum (MCAO) and sensorimotor cortex (PT). Pellet retrieval was altered in both cases but did not correlate with stroke volume or ischemia extent. Instead, cortical ischemia was characterized by increased hand slips and modified reaching success. Striatal ischemia led to progressively prolonged reach durations, mirroring delayed symptom onset in basal ganglia strokes. In summary, refined machine learning-based movement analysis revealed specific deficits in mice after cortical and striatal ischemia. These findings emphasize the importance of thorough behavioral profiling in preclinical stroke research to increase translational validity of behavioral assessments.

neuroscience↗

bioRxiv2023

Pial collaterals develop through mosaic colonization of capillaries by arterial and microvascular endothelial cells

Collaterals are unique blood vessels present in many healthy tissues that cross-connect distal-end arterioles of adjacent arterial trees, thus providing alternate routes of perfusion. Stroke patients with superior pial collateral flow respond better to treatments and present with an overall improved prognostic outcome. However, how pial collaterals develop in the embryo and how they reactivate upon stroke remains unclear. Here, using lineage tracing in combination with three-dimensional imaging, we demonstrate that mouse embryos employ a novel mechanism to build pial collaterals, distinct from their outward remodeling following stroke. Endothelial cells (ECs) of arterial and microvascular origin invade already existing pre-collateral vascular structures in a process which we termed mosaic colonization. Arterialization of these pre-collateral vascular segments happens concurrently with mosaic colonization. Despite having a smaller proliferative capacity, embryonic arterial cells represent the majority of cells that migrate to form nascent collaterals; embryonic microvascular cells, despite their higher proliferative potential, form only about a quarter of collateral endothelial cells. Moreover, postnatal collateral growth relies much more on self-replenishment of arterial cells than on microvascular contribution. Following ischemic injury, pial collateral outward remodeling relies on local cell proliferation rather than recruitment of non-arterial cells. Together, these findings establish distinct cellular mechanisms underlying pial collateral development and ischemic remodeling, raising the prospect for future research to identify novel, collateral-specific therapeutic strategies for ischemic stroke.

developmental biology↗

bioRxiv2022

Deep learning-based automated lesion segmentation on mouse stroke magnetic resonance images

Magnetic resonance imaging (MRI) is widely used for ischemic stroke lesion detection in mice. A challenge is that lesion segmentation often relies on manual tracing by trained experts, which is labor-intensive, time-consuming, and prone to inter- and intra-rater variability. Here, we present a fully automated ischemic stroke lesion segmentation method for mouse T2-weighted MRI data. As an end-to-end deep learning approach, the automated lesion segmentation requires very little preprocessing and works directly on the raw MRI scans. We randomly split a large dataset of 382 MRI scans into a subset (n = 293) to train the automated lesion segmentation and a subset (n = 89) to evaluate its performance. We compared Dice coefficients and accuracy of lesion volume against manual segmentation, as well as its performance on an independent dataset from an open repository with different imaging characteristics. The automated lesion segmentation produced segmentation masks with a smooth, compact, and realistic appearance that are in high agreement with manual segmentation.

neuroscience↗

bioRxiv2022

Prediction of Stroke Outcome in Mice Based on Non-Invasive MRI and Behavioral Testing

BackgroundPrediction of post-stroke outcome using the degree of subacute deficit or magnetic resonance imaging is well studied in humans. While mice are frequently used animals in preclinical stroke research, systematic analysis of outcome predictors is lacking. MethodsWe introduced heterogeneity into our study to broaden the applicability of our prediction tools. We analyzed the effect of 30, 45 and 60 minutes of arterial occlusion on the variance of stroke volumes. Next, we built a heterogeneous cohort of 215 mice using data from 15 studies that included 45 minutes of middle cerebral artery occlusion and various genotypes. Motor function was measured using the staircase test of skilled reaching. Phases of subacute and residual deficit were defined. Magnetic resonance images of stroke lesions were co-registered on the Allen Mouse Brain Atlas to characterize stroke topology. Different random forest prediction models that either used motor-functional deficit or imaging parameters were generated for the subacute and residual deficits. ResultsVariance of stroke volumes was increased by 45 minutes of arterial occlusion compared to 60 minutes and including various genotypes. We detected both a subacute and residual motor-functional deficit after stroke and different recovery trajectories. In mice with small cortical lesions, lesion volume was the best predictor of the subacute deficit. The residual deficit was most accurately predicted by the degree of the subacute deficit. When using imaging parameters for the prediction of the residual deficit, including information about the lesion topology increased prediction accuracy. A subset of anatomical regions within the ischemic lesion had particular impact on the prediction of long-term outcome. ConclusionsWe developed and validated a robust tool for the prediction of functional outcome after stroke in mice using a large heterogeneous cohort. Study design and imaging limitations are discussed. In the future, using outcome prediction can improve the design of preclinical studies and guide intervention decisions.

neuroscience↗

bioRxiv2021

Quantification of allosteric communications in matrix metalloprotease-1 on alpha-synuclein aggregates and substrate-dependent virtual screening

Alpha-synuclein (aSyn) has implications in pathological protein aggregations observed in neurodegenerative disorders, including Parkinsons and Alzheimers diseases. There are currently no approved prevention and cure for these diseases. In this context, matrix metalloproteases (MMPs) provide an opportunity because MMPs are broad-spectrum proteases and cleave aSyn. Previously, we showed that allosteric communications between the two domains of MMP1 on collagen fibril and fibrin depend on substrates, MMP1 activity, and ligands. However, allosteric communications in MMP1 on aSyn-induced aggregates have not been explored. Here we report quantification of allostery using single molecule measurements of MMP1 dynamics on aSyn-induced aggregates by calculating Forster Resonance Energy Transfer (FRET) between two dyes attached to the catalytic and hemopexin domains of MMP1. The two domains of MMP1 prefer open conformations, with the two domains well-separated. These open conformations are inhibited by a single point mutation E219Q of MMP1 and tetracycline, an MMP inhibitor. A two-state Poisson process describes the interdomain dynamics. The best-fit parameters for a Gaussian fit to the distributions of FRET values provide the two states. The ratio of the kinetic rates between the two states comes from the ratio of fitted areas around the two states. The decay rate of an exponential fit to the correlations between FRET values provides the sum of the kinetic rates. Since a crystal structure of aSyn-bound MMP1 is not available, we performed molecular docking of MMP1 with aSyn using ClusPro. We simulated MMP1 dynamics using different docking poses and matched the experimental and simulated interdomain dynamics to determine the most appropriate pose. We performed virtual screening against the potential ligand-binding sites on the appropriate aSyn-MMP1 binding pose and showed that lead molecules differ between free MMP1 and substrate-bound MMP1. In other words, virtual screening needs to take substrates into account for substrate-specific control of MMP1 activity. Molecular understanding of interactions between MMP1 and aSyn-induced aggregates may open up the possibility of degrading pathological aggregates in neurodegeneration by targeting MMPs. SignificanceWe have quantified MMP1 interdomain dynamics on aSyn-induced aggregates by a two-state Poisson process. Histograms and correlations of FRET values determine the kinetic rates of interconversion between the two states. We quantify the conformational dynamics of the whole MMP1 and allosteric communications by the two-dimensional matrix of correlations between every pair of amino acids from experimentally-validated all-atom simulations. The two-dimensional correlations lead to a Gray Level Co-occurrence Matrix and a measure of Shannon entropy describing the conformational fluctuations. As such, we address the quantification of allosteric communications, a leading challenge in defining allostery. We report that the potential ligand-binding sites and lead molecules change for MMP1 upon binding alpha-synuclein and depend on the binding pose selected. This suggests that one needs to take the substrate into account while targeting MMPs.

biophysics↗

bioRxiv2020

Vascular cognitive impairment in the mouse reshapes visual, spatial network functional connectivity.

Connectome analysis of neuroimaging data is a rapidly expanding field to identify disease specific biomarkers. Structural diffusion MRI connectivity has been useful in individuals with radiological features of small vessel disease, such as white matter hyperintensities. Global efficiency, a network metric calculated from the structural connectome, is an excellent predictor of cognitive decline. To dissect the biological underpinning of these changes, animal models are required. We tested whether the structural connectome is altered in a mouse model of vascular cognitive impairment. White matter damage was more pronounced by 6 compared to 3 months. Global efficiency remained intact, but the visual association cortex exhibited increased structural connectivity with other brain regions. Exploratory resting state functional MRI connectivity analysis revealed diminished default mode network activity in the model compared to shams. Further perturbations were observed in a primarily cortical hub and the retrosplenial and visual cortices, and the hippocampus were the most affected nodes. Behavioural deficits were observed in the cued water maze, supporting the suggestion that the visual and spatial memory networks are affected. We demonstrate specific circuitry is rendered vulnerable to vascular stress in the mouse, and the model will be useful to examine pathophysiological mechanisms of small vessel disease. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

neuroscience↗

bioRxiv2020

Selective inhibition of histone deacetylase 1 and 3 improves motor phenotype and alleviates transcriptional dysregulation in Huntington's disease mice

Huntingtons disease (HD) is an autosomal dominant neurodegenerative disease characterized by a late clinical onset of psychiatric, cognitive, and motor symptoms. Transcriptional dysregulation is an early and central disease mechanism which is accompanied by epigenetic alterations in HD. Previous studies demonstrated that targeting transcriptional changes by inhibition of histone deacetylases (HDACs), especially the class I HDACs, provides therapeutic effects. Yet, their exact mechanisms of action and the features of HD pathology, on which these inhibitors act remain to be elucidated. Here, using transcriptional profiling, we found that selective inhibition of HDAC1 and HDAC3 by RGFP109 repaired the expression of a number of genes, including the transcription factor genes Neurod2 and Nr4a2, and 43% of the gene sets that were dysregulated by mutant Huntingtin expression in the striatum and improved motor skill learning deficit in the R6/1 mouse model of HD. RGFP109-treated R6/1 mice showed improved coordination on the RotaRod over four consecutive trials, while vehicle-treated R6/1 animals displayed no improvement in coordination skills and fell 50 seconds earlier off the rod in the fourth trial. We also found, by volumetric MRI, a widespread brain atrophy in the R6/1 mice at the symptomatic disease stage, on which RGFP109 showed a modest effect. Collectively, our combined work presents new evidence for specific HDAC1 and HDAC3 inhibition as a therapeutic strategy for alleviating the phenotypic and molecular features of HD.

neuroscience↗

bioRxiv2020

C-terminal-dependent control of EAAT2 signaling, corticostriatal synaptic glutamate clearance and spontaneous motor activity in mice with hypokinesia

Rapid removal of glutamate from the sites of glutamate release is an essential step in excitatory synaptic transmission. Despite many years of research, the molecular mechanisms underlying the intracellular regulation of glutamate transport at tripartite synapses have remained unclear. This limits the options for pharmacological treatment of motor disorders associated with glutamate excitotoxicity. Therefore, using the Q175 mouse model of Huntingtons disease (HD), we explored the effects of structural changes in the astrocytic excitatory amino acid transporter type 2 (EAAT2). We report that expression of a C-terminal-modified variant of EAAT2 can alleviate the symptoms of hypokinesia in mice with already advanced HD. At a cellular level, this beneficial outcome correlated with faster synaptic glutamate clearance, higher astrocytic glutamate uptake and larger amounts of native EAAT2 protein. Proteomics data indicate a partial reversal of HD-induced changes in the EAAT2 interactor spectrum. Thus, astrocytic glutamate transport remains a target for therapeutic intervention.

neuroscience↗

bioRxiv2020

Serotonin suppresses slow oscillations by activating somatostatin interneurons via the 5-HT2A receptor

Serotonin (5-HT) is one of the major neuromodulators present in the mammalian brain and has been shown to play a role in multiple physiological processes. The mechanisms by which 5-HT modulates cortical network activity, however, are not yet fully understood. We investigated the effects of 5-HT on slow oscillations (SOs), a synchronized cortical network activity universally present across species. SOs are observed during anesthesia and are considered to be the default cortical activity pattern. We discovered that ({+/-})3,4-methylenedioxymethamphetamine (MDMA) and fenfluramine, two potent 5-HT releasers, inhibit SOs within the entorhinal cortex (EC) in anesthetized mice. Combining opto- and pharmacogenetic manipulations with in vitro electrophysiological recordings, we uncovered that somatostatin-expressing (Sst) interneurons activated by the 5-HT2A receptor (5-HT2AR) play an important role in the suppression of SOs. Since 5-HT2AR signaling is involved in the etiology of different psychiatric disorders and mediates the psychological effects of many psychoactive serotonergic drugs, we propose that the newly discovered link between Sst interneurons and 5-HT will contribute to our understanding of these complex topics.

neuroscience↗

bioRxiv2019

Fibrinolytic activity of matrix metalloprotease-1

The roles of protein conformational dynamics and allostery in function are well-known. However, the roles that inter-domain dynamics have in function are not entirely understood. We used matrix metalloprotease-1 (MMP1) as a model system to study the relationship between inter-domain dynamics and activity because MMP1 has diverse substrates. Here we focus on fibrin, the primary component of a blood clot. Water-soluble fibrinogen, following cleavage by thrombin, self-polymerize to form water-insoluble fibrin. We studied the inter-domain dynamics of MMP1 on fibrin without crosslinks using single-molecule Forster Resonance Energy Transfer (smFRET). We observed that the distance between the catalytic and hemopexin domains of MMP1 increases or decreases as the MMP1 activity increases or decreases, respectively. We modulated the activity using 1) an active site mutant (E219Q) of MMP1, 2) MMP9, another member of the MMP family that increases the activity of MMP1, and 3) tetracycline, an inhibitor of MMP1. We fitted the histograms of smFRET values to a sum of two Gaussians and the autocorrelations to an exponential and power law. We modeled the dynamics as a two-state Poisson process and calculated the kinetic rates from the histograms and autocorrelations. Activity-dependent inter-domain dynamics may enable allosteric control of the MMP1 function.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2019

Allosteric communications between domains modulate activity of matrix metalloprotease-1

An understanding of the structure-dynamics relationship is essential for understanding how a protein works. Prior research has shown that the activity of a protein correlates with intra-domain dynamics occurring at picosecond to millisecond timescales. However, the correlation between inter-domain dynamics and the function of a protein is poorly understood. Here we show that communications between the catalytic and hemopexin domains of matrix metalloprotease-1 (MMP1) on type-1 collagen fibrils correlate with its activity. Using single-molecule FRET (smFRET), we identified functionally relevant open conformations where the two MMP1 domains are well-separated, which were significantly absent for catalytically inactive point mutant (E219Q) of MMP1 and could be modulated by an inhibitor or an enhancer of activity. The observed relevance of open conformations resolves the debate about the roles of open and closed MMP1 structures in function. A sum of two Gaussians fitted histograms, whereas an exponential fitted autocorrelations of smFRET values. We used a two-state Poisson process to describe the dynamics and used histograms and autocorrelations of conformations to calculate the kinetic rates between the two states. All-atom and coarse-grained simulations reproduced some of the experimental features and revealed substrate-dependent MMP1 dynamics. Our results suggest that an inter-domain separation facilitates opening up the catalytic pocket so that the collagen chains come closer to the MMP1 active site. Coordination of functional conformations at different parts of MMP1 occurs via allosteric communications that can take place via interactions mediated by collagen even if the linker between the domains is absent. Modeling dynamics as a Poisson process enables connecting the picosecond timescales of molecular dynamics simulations with the millisecond timescales of single molecule measurements. Water-soluble MMP1 interacting with water-insoluble collagen fibrils poses challenges for biochemical studies that the single molecule tracking can overcome for other insoluble substrates. Inter-domain communications are likely important for multidomain proteins. Statement of SignificanceIt is often challenging to distinguish functionally important dynamics because proteins are inherently flexible. MMP1 is a model enzyme because both the catalytic and hemopexin domains are necessary to degrade triple-helical type-1 collagen, the highly proteolysis-resistant structural component of the extracellular matrix. We report, for the first time, measurements of MMP1 inter-domain dynamics on type-1 collagen fibrils. We have identified functionally relevant MMP1 conformations where the two domains are far apart. Mutations and ligands can allosterically modulate the dynamics that correlate with activity. The dynamics follow a two-state Poisson process that connects the picosecond timescales of MD simulations with the millisecond timescales of experiments. The two domains can functionally communicate via collagen even when the physical linker is absent.

biophysics↗