Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies

Abstract

BackgroundGuanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. Scope of reviewWe review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles. Major conclusionsThe KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQforming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables. General significanceWe reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes.

Stability of Two-quartet G-quadruplexes and Their Dimers in Atomistic Simulations

“…These force-field versions include also earlier essential DNA [56][57][58] and RNA 56 modifications of the original AMBER Cornell et al nucleic acids force-field; 59 for more details see refs. 42,60 The starting structures were equilibrated using standard protocols described in the Supporting Information. The simulations were performed with PMEMD CUDA version of AMBER16.…”

“…This may be partly caused by the differences in the ions and water models, though most likely it primarily reflects the known multidimensionality of the freeenergy landscape. 42 The first GQ unit unfolded by strand slippage and rotation leading to the formation of cross like structure in Na + and K + ions in SPC/E water model and K + ions in OPC water model (Table 1 and Figure 3). Strand slippage is a movement of a strand by one step up or down, reducing the number of full quartets by one.…”

“…60 Generally, outcomes of simulation studies of fully folded cation-stabilized GQ structures are often unaffected by these imbalances, due to the extraordinary stability and stiffness of GQs. 42 Simulations with appropriate force fields starting from fully folded cation-stabilized GQs are usually entirely stable, as their life-times, even as described by the force field, extend far beyond the simulation time scale. In contrast, any larger perturbation of the quartets in simulations of GQ structures derived from experiments indicate that an inadequate force field has been used.…”

“…MD methodology, when wisely applied, can provide useful insights into various aspects of GQ structural dynamics and folding. 42 While the contemporary MD is not robust enough to quantitatively evaluate the absolute stability of the GQs in a thermodynamic sense, the simulations should fairly well reflect different relative structural stabilities of GQ arrangements, provided the simulation time scale is sufficiently long to see structural perturbations and unfolding in the simulations, i.e., to assess the lifetimes (1/k off ) of the studied arrangements. We have carried out the simulations with both Na + and K + as the stabilizing cations to analyse and compare the cation dynamics.…”

Computational Methods to Study G-Quadruplex–Ligand Complexes

“…87 This can result in the stabilisation of bifurcated H-bonds, close amino group contacts, non-planar G/A base pairs and some other specific interactions. 87,89,90 The force fields assume purely sp 2 amino hybridisation for ring nitrogen atoms. This should be sufficient for most interactions, as primary H-bonds stabilize the sp 2 electronic structure.…”