Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

Réblová, Kamila; Fadrná, Eva; Sarzyñska, Joanna; Kuliński, Tadeusz; Kulhánek, Petr; Ennifar, Eric; Koča, Jaroslav; Šponer, Jiřı́

doi:10.1529/biophysj.107.110056

Cited by 54 publications

(88 citation statements)

References 102 publications

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“…The production MD runs were carried out with constant pressure boundary conditions (relaxation time of 1.0 ps). Our methods for equilibration and production run protocols are described in greater detail elsewhere (33,74,77,78). Translational and rotational center-of-mass motions were initially removed, and periodically, simulations were interrupted to have the center-ofmass removed again by a subtraction of velocities to account for the "flying ice cube" effect (79).…”

Section: Unbiased Molecular Dynamics Simulationsmentioning

confidence: 99%

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis

Kayode

Wang

Pendlebury

et al. 2016

Journal of Biological Chemistry

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Edited by George DeMartinoThe molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsinproduct complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and productlike states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.Protein function is determined by macromolecular geometry conferred by the folded state, as noted by Anfinsen nearly 40 years ago (1); however, recent years have brought fresh meaning to this paradigm with an increasing appreciation of the temporal dependence of protein structure. Proteins constantly sample varied conformational fluctuations about the time-averaged structures that we observe crystallographically or spectroscopically, and these conformational dynamics are in many cases closely coupled to protein function (2-4). Nowhere is this clearer than for enzymes, proteins evolved to accelerate biological chemical reactions. Varied examples have revealed that enzyme conformational dynamics can facilitate substrate binding, progression along the catalytic reaction coordinate, and product release (5-10). Most studies of protein dynamics in enzyme catalysis have naturally focused on conformational changes within the enzyme. However, for the many enzymes that catalyze reactions of protein substrates, an overlooked source of potentially relevant dynamics lies within the substrate.Trypsins are serine proteases, a class of proteolytic enzymes that have been well characterized and used to dissect and understand catalysis, most often using short oligopeptide model substrates as proxies for natural protein substrates. Following formation of a noncovalent Michaelis complex, the catalytic mechanism proceeds through two sequential steps (Scheme 1) (11). In the first step, the enzyme serine...

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Section: Unbiased Molecular Dynamics Simulationsmentioning

confidence: 99%

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis

Kayode

Wang

Pendlebury

et al. 2016

Journal of Biological Chemistry

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“…Similar short-comings apply to an all-atom study of the flanking bases in RNA kissing-complexes, which noted some transitions from configurations where the bulge bases are inserted into the helix to configurations where the bases are flipped out. 45 A noteworthy all-atom study of RNA molecules containing varying bulge sizes observed the presence of a wobble G-U base pair flanking the bulge that increased flexibility of the structure when compared with a Watson-Crick G-C base pair in the same location. 46 As noted earlier, the oxDNA potential cannot capture the influence of non-Watson-Crick interactions on flexibility in bulged systems.…”

Section: Comparison With Experiments and All-atom Simulationsmentioning

confidence: 99%

“…29,[40][41][42] The degree of coarse-graining in oxDNA allows us to study the equilibrium ensemble of junction configurations, which involves observing substantial structural transitions at the junction repeatedly for each system. All-atom investigations of DNA and RNA systems containing bulges [44][45][46] have not yet been performed with this scope, due to the cost of simulating allatom force fields.…”

Section: Introductionmentioning

confidence: 99%

Characterizing the bending and flexibility induced by bulges in DNA duplexes

Schreck

Ouldridge

Romano

et al. 2015

The Journal of Chemical Physics

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Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight and the bulge is on one side of the duplex, and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures.

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“…49,51,[54][55][56] Other RNA kissing motifs were also studied by means of MD, including H3 stem-loop of Moloney murine leukemia virus, 46 TAR elements of HIV 31,57 and kissing complex from 23 rRNA. 58 Due to inconsistency among the previously published results for simulations of DIS kissing complexes and availability of new experimental structures we were motivated to substantially extend theoretical studies of kissing complexes. We have performed multiple simulations (close to 1 ls of total) using different starting experimental structures, different ion conditions and AMBER and CHARMM force fields.…”

mentioning

confidence: 99%

Conformational transitions of flanking purines in HIV‐1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics

et al. 2008

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Dimerization of HIV-1 genomic RNA is initiated by kissing loop interactions at the Dimerization Initiation Site (DIS). Dynamics of purines that flank the 5' ends of the loop-loop helix in HIV-1 DIS kissing complex were explored using explicit solvent molecular dynamics (MD) simulations with the CHARMM force field. Multiple MD simulations (200 ns in total) of X-ray structures for HIV-1 DIS Subtypes A, B, and F revealed conformational variability of flanking purines. In particular, the flanking purines, which in the starting X-ray structures are bulged-out and stack in pairs, formed a consecutive stack of four bulged-out adenines at the beginning of several simulations. This conformation is seen in the crystal structure of DIS Subtype F with no interference from crystal packing, and was frequently reported in our preceding MD studies performed with the AMBER force field. However, as CHARMM simulations progressed, the four continuously stacked adenines showed conformational transitions from the bulged-out into the bulged-in geometries. Although such an arrangement has not been seen in any X-ray structure, it has been suggested by a recent NMR investigation. In CHARMM simulations, in the longer time scale, the flanking purines display the tendency to move to bulged-in conformations. This is in contrast with the AMBER simulations, which indicate a modest prevalence for bulged-out flanking base positions in line with the X-ray data. The simulations also suggest that the intermolecular stacking between purines from the opposite hairpins can additionally stabilize the kissing complex.

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Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

Cited by 54 publications

References 102 publications

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis

Characterizing the bending and flexibility induced by bulges in DNA duplexes

Conformational transitions of flanking purines in HIV‐1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics

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