Abstract
BackgroundStructural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Methodology/Principal FindingsMolecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined) base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.Conclusions/SignificanceThe calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5′ and 3′ directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.
Highlights
Biological macromolecules and their complexes often undergo large structural changes during their functional cycles [1,2]
Irrespective of which category the structural changes belong to, a quantitative method that could identify and characterize the energetics of structural changes at the precision level of well-defined local degrees of freedom is highly desirable. Many experimental methods such as X-ray crystallography [5] or Nuclear Magnetic Resonance (NMR) Spectroscopy [6] can identify the atomic details of stable states involved in the structural changes
Conformational analysis using free energy landscapes This study focuses on readily visualizing and quantifying the range of conformational space sampled by local degrees of freedom during a structural change in the macromolecule; which in the present case is the flipping of a base out of a DNA duplex
Summary
Biological macromolecules and their complexes often undergo large structural changes during their functional cycles [1,2]. Irrespective of which category the structural changes belong to, a quantitative method that could identify and characterize the energetics of structural changes at the precision level of well-defined local degrees of freedom is highly desirable. Many experimental methods such as X-ray crystallography [5] or Nuclear Magnetic Resonance (NMR) Spectroscopy [6] can identify the atomic details of stable states involved in the structural changes. Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes
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