Browsing by Author "Berlaga, Alex"

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    Copper-mediated peptide arylation selective for the N-terminus
    (Royal Society of Chemistry, 2020) Miller, Mary K.; Wang, Haopei; Hanaya, Kengo; Zhang, Olivia; Berlaga, Alex; Ball, Zachary T.
    Polypeptides present remarkable selectivity challenges for chemical methods. Amino groups are ubiquitous in polypeptide structure, yet few paradigms exist for reactivity and selectivity in arylation of amine groups. This communication describes the utilization of boronic acid reagents bearing certain o-electron withdrawing groups for copper-mediated amine arylation of the N-terminus under mild conditions and primarily aqueous solvent. The method adds to the toolkit of boronic acid reagents for polypeptide modification under mild conditions in water that shows complete selectivity for the N-terminus in the presence of lysine side chains.
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    Molecular Mechanisms of Active Transport in Antiporters: Kinetic Constraints and Efficiency
    (American Chemical Society, 2021) Berlaga, Alex; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics
    A vital role in supporting successful functioning of biological cells is played by membrane channels called antiporters. These channel proteins utilize the concentration gradient of one type of species to move another type of species in the opposite direction and against their concentration gradient. It is believed that antiporters operate via alternating conformational transitions that expose these proteins to different sides of the membrane, and that only thermodynamics controls the activation of these channels. Here we explicitly investigate a chemical-kinetic model of antiporters to argue that there are additional kinetic constraints that need to be satisfied for these channels to be operational. This implies that kinetics and not thermodynamics governs the functioning of antiporters. In addition, the efficiency of antiporters is analyzed and the most optimal operating conditions are discussed. Our theoretical analysis clarifies some important aspects of the molecular mechanisms of biological membrane transport.
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    Theoretical study of active secondary transport: Unexpected differences in molecular mechanisms for antiporters and symporters
    (AIP Publishing LLC, 2022) Berlaga, Alex; Kolomeisky, Anatoly B.; Center for Theoretical Biological Physics
    Successful functioning of biological cells relies on efficient translocation of different materials across cellular membranes. An important part of this transportation system is membrane channels that are known as antiporters and symporters. They exploit the energy stored as a trans-membrane gradient of one type of molecules to transport the other types of molecules against their gradients. For symporters, the directions of both fluxes for driving and driven species coincide, while for antiporters, the fluxes move in opposite directions. There are surprising experimental observations that despite differing only by the direction of transport fluxes, the molecular mechanisms of translocation adopted by antiporters and symporters seem to be drastically different. We present chemical-kinetic models to quantitatively investigate this phenomenon. Our theoretical approach allows us to explain why antiporters mostly utilize a single-site transportation when only one molecule of any type might be associated with the channel. At the same time, the transport in symporters requires two molecules of different types to be simultaneously associated with the channel. In addition, we investigate the kinetic constraints and efficiency of symporters and compare them with the same properties of antiporters. Our theoretical analysis clarifies some important physical–chemical features of cellular trans-membrane transport.