Marek Orzechowski

Broad Institute of MIT and Harvard · Cancer Program

The ability to measure neutralizing antibodies on large scale can be important for understanding features of the natural history and epidemiology of infection, as well as an aid in determining the efficacy of interventions, particularly in outbreaks such as the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Because o...

Background Unbiased assessment of risks associated with acquisition of SARS-CoV-2 is critical to informing mitigation efforts during pandemics. The objective of our study was to understand the risk factors for acquiring COVID-19 in a large, prospective cohort of adult residents in a large US metropolitan area. Methods We designed a fully remote, l...

Importance: Unbiased assessment of risks associated with acquisition of SARS-CoV-2 is critical to informing mitigation efforts during pandemics. Objective: Understand risk factors for acquiring COVID-19 in a large, prospective cohort of adult residents recruited to be representative of a large US metropolitan area. Design: Fully remote longitu...

Background Antibody response duration following SARS-CoV-2 infection tends to be variable and depends on severity of disease and method of detection. Study design and methods COVID-19 convalescent plasma (CCP) from 18 donors was collected longitudinally for a maximum of 63 - 129 days following resolution of symptoms. All the samples were initially...

The efficacies of all antibiotics against tuberculosis are eventually eroded by resistance. New strategies to discover drugs or drug combinations with higher barriers to resistance are needed. Previously, we reported the application of a large-scale chemical-genetic interaction screening strategy called PROSPECT to the discovery of new Mycobacteriu...

The efficacies of all antibiotics against tuberculosis are eventually eroded by resistance. New strategies to discover drugs or drug combinations with higher barriers to resistance are needed. Previously, we reported the application of a large-scale chemical-genetic interaction screening strategy called PROSPECT to the discovery of new Mycobacteriu...

Calcium regulation of cardiac muscle contraction is controlled by the thin-filament proteins troponin and tropomyosin bound to actin. In the absence of calcium, troponin-tropomyosin inhibits myosin-interactions on actin and induces muscle relaxation, whereas the addition of calcium relieves the inhibitory constraint to initiate contraction. Many mu...

We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs, and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high-throughput reduced representation expression pr...

We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high throughput reduced representation expression pro...

Azimuthal movement of tropomyosin around the F-actin thin filament is responsible for muscle activation and relaxation. Our model of alpha-tropomyosin, derived from molecular-mechanics and electron microscopy of different contractile states, indicates that tropomyosin is rather stiff and pre-bent to present one specific face to F-actin during azimu...

Coiled-coil tropomyosin binds super-helically along F-actin. Together with the troponin complex, tropomyosin inhibits myosin-binding. McKillop and Geeves (1993) introduced a three-state model for thin filament regulation with tropomyosin occupying three positions on the actin filament; blocked, closed and open. In the absence of myosin, tropomyosin...

Azimuthal movement of tropomyosin around the F-actin thin filament is responsible for muscle activation and relaxation. Recently a model of αα-tropomyosin, derived from molecular-mechanics and electron microscopy of different contractile states, showed that tropomyosin is rather stiff and pre-bent to present one specific face to F-actin during azim...

Tropomyosin regulates a wide variety of actin filament functions and is best known for the role that it plays together with troponin in controlling muscle activity. For effective performance on actin filaments, adjacent 42-nm-long tropomyosin molecules are joined together by a 9- to 10-residue head-to-tail overlapping domain to form a continuous ca...

To be effective as a gatekeeper regulating the access of binding proteins to the actin filament, adjacent tropomyosin molecules associate head-to-tail to form a continuous super-helical cable running along the filament surface. Chimeric head-to-tail structures have been solved by NMR and X-ray crystallography for N- and C-terminal segments of smoot...

Muscle contraction is regulated by troponin-tropomyosin, which blocks and unblocks myosin binding sites on actin. To elucidate this regulatory mechanism, the three-dimensional organization of troponin and tropomyosin on the thin filament must be determined. Although tropomyosin is well defined in electron microscopy helical reconstructions of thin...

Muscle contraction is regulated by tropomyosin movement across the thin filament surface, which exposes or blocks myosin-binding sites on actin. Recent atomic structures of F-actin-tropomyosin have yielded the positions of tropomyosin on myosin-free and myosin-decorated actin. Here, the repositioning of -tropomyosin between these locations on F-act...

Coiled-coil tropomyosin, localized on actin filaments in virtually all eukaryotic cells, serves as a gatekeeper regulating access of the motor protein myosin and other actin-binding proteins onto the thin filament surface. Tropomyosin's modular pseudo-repeating pattern of approximately 39 amino acid residues is designed to allow binding of the coil...

Our thesis is that thin filament function can only be fully understood and muscle regulation then elucidated if atomic structures of the thin filament are available to reveal the positions of tropomyosin on actin in all physiological states. After all, it is tropomyosin influenced by troponin that regulates myosin-crossbridge cycling on actin and t...

The energy landscape describing the movement of tropomyosin on the actin filament was determined computationally for a set of tropomyosin positions on the surface of wild-type and mutant actin (K326N, E334K, D25N). All the mutations studied, have been detected in individuals with various myopathies and analysis of changes in the energy-landscapes m...

At low-Ca2+, tropomyosin is pinned-down on thin filaments by troponin-I to block myosin-binding sites, crossbridge-cycling and contraction, while at high-Ca2+, troponin and myosin push tropomyosin azimuthally to expose these sites. Energy landscape measurements diagram a wide minimum for positioning tropomyosin on actin-subunits, which is establish...

Muscle contraction is regulated by movement of tropomyosin over the surface of actin filaments. At low-Ca2+, tropomyosin blocks myosin-binding on actin, whereas, in a two-step process, Ca2+-saturated troponin and myosin open the myosin-binding site leading to contraction. No obvious steric obstructions or geometrical barriers on actin limit such tr...

Using mechanical unfolding by optical tweezers (OT) and steered molecular dynamics (SMD) simulations, we have demonstrated the critical role of Mg(2+) ions for the resistance of the Beet Western Yellow Virus (BWYV) pseudoknot (PK) to unfolding. The two techniques were found to be complementary, providing information at different levels of molecular...

The formation, stability, and dynamics of water filaments in disordered environments is investigated by using atomistic molecular dynamics simulations. It is found that in an alkyl-chain arrangement representative of that used in liquid chromatography, extended water filaments can form for up to 1 ns before they are destroyed again due to thermal f...

Mechanical unfolding of −1 frameshift signals such as RNA pseudoknots have aimed to test the hypothesis that the stability of the pseudoknot (PK) is directly correlated to the frameshifting efficiency. Here we report unfolding of the Beet Western Yellow Virus (BWYV) PK by optical tweezers complemented by computer simulations using steered molecular...

Several approaches have been introduced to interpret, in terms of high-resolution structure, low-resolution structural data as obtained from cryo-EM. As conformational changes are often observed in biological molecules, these techniques need to take into account the flexibility of proteins. Flexibility has been described in terms of movement betwee...

A methodology for flexible fitting of all-atom high-resolution structures into low-resolution cryoelectron microscopy (cryo-EM) maps is presented. Flexibility of the modeled structure is simulated by classical molecular dynamics and an additional effective potential is introduced to enhance the fitting process. The additional potential is proportio...

We present the preliminary results of two computer experiments involving the application of an external force to molecular systems. In the first experiment we simulated the process of pulling out a simple intercalator, the 9-aminoacridine molecule, from its complex with a short DNA oligonucleotide in aqueous solution. Removing a drug from the DNA i...

The coiled-coil stability and rigidity may be of importance for molecular electronics (electronically bistable molecules). The coiled-coil binding free energy has been calculated using molecular dynamics (MD). The energy has been computed as a difference of the appropriate free energies; derived for the coiled-coil and isolated alpha-helices separa...