Literature DB >> 26801011

Perspective: Mechanochemistry of biological and synthetic molecules.

Dmitrii E Makarov1.   

Abstract

Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then to describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field.

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Year:  2016        PMID: 26801011     DOI: 10.1063/1.4939791

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  12 in total

1.  Mean Direct-Transit and Looping Times as Functions of the Potential Shape.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Phys Chem B       Date:  2017-05-17       Impact factor: 2.991

2.  A new insight into diffusional escape from a biased cylindrical trap.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2017-09-14       Impact factor: 3.488

3.  First passage, looping, and direct transition in expanding and narrowing tubes: Effects of the entropy potential.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2017-10-07       Impact factor: 3.488

4.  Assessing models of force-dependent unbinding rates via infrequent metadynamics.

Authors:  Willmor J Peña Ccoa; Glen M Hocky
Journal:  J Chem Phys       Date:  2022-03-28       Impact factor: 3.488

5.  Molecular Paradigms for Biological Mechanosensing.

Authors:  David Gomez; Willmor J Peña Ccoa; Yuvraj Singh; Enrique Rojas; Glen M Hocky
Journal:  J Phys Chem B       Date:  2021-10-28       Impact factor: 3.466

6.  Size extensivity of elastic properties of alkane fragments.

Authors:  Milad Radiom; Plinio Maroni; Tomasz A Wesolowski
Journal:  J Mol Model       Date:  2018-01-08       Impact factor: 1.810

7.  Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins.

Authors:  Stanislav M Avdoshenko; Atanu Das; Rohit Satija; Garegin A Papoian; Dmitrii E Makarov
Journal:  Sci Rep       Date:  2017-03-21       Impact factor: 4.379

8.  Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force.

Authors:  J P Renn; S Bhattacharyya; H Bai; C He; H Li; A F Oberhauser; J F Marko; D E Makarov; A Matouschek
Journal:  Sci Rep       Date:  2019-07-31       Impact factor: 4.379

9.  Theoretical simulation of the infrared signature of mechanically stressed polymer solids.

Authors:  Matthew S Sammon; Milan Ončák; Martin K Beyer
Journal:  Beilstein J Org Chem       Date:  2017-08-17       Impact factor: 2.883

Review 10.  Mechanochemistry of nucleosides, nucleotides and related materials.

Authors:  Olga Eguaogie; Joseph S Vyle; Patrick F Conlon; Manuela A Gîlea; Yipei Liang
Journal:  Beilstein J Org Chem       Date:  2018-04-27       Impact factor: 2.883

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