Ribose puckering:  structure, dynamics, energetics, and the pseudorotation cycle

Harvey, Stephen C.; Prabhakaran, M.

doi:10.1021/ja00280a004

Cited by 112 publications

(56 citation statements)

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“…Applying ab initio calculations on models of the deoxyribose derived from this study, we found that there is an ~4 kcal/mol energy barrier (primarily bonding energy) at the O4'-endo intermediate step. This is lower than the ~5-6 kcal/mol estimated for planar intermediates required for a direct conversion from C2'-to C3'-endo, and is similar to estimates from experimental (Olson and Sussman, 1982) and other ab initio calculations (Foloppe et al, 2001) on the barrier (although about 2-fold higher than molecular dynamics estimates (Arora and Schlick, 2003;Harvey and Prabhakaran, 1986)). Associated with the changes in sugar pucker are perturbations to the base stacking.…”

Section: Going From B To Asupporting

confidence: 78%

DNA Structure: Alphabet Soup for the Cellular Soul

Ho¹,

Carter²

2011

DNA Replication-Current Advances

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Section: Going From B To Asupporting

confidence: 78%

DNA Structure: Alphabet Soup for the Cellular Soul

Ho¹,

Carter²

2011

DNA Replication-Current Advances

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“…Harvey and Prabhakaran have shown when describing the ribose ring puckering, p m and P m are linearly correlated at each puckering state although their values are not exactly same. 31 In addition, q m and Q m are also related, and their relation can be approximated by a simple equation: 32…”

Section: Theorymentioning

confidence: 99%

“…(2) and (4), both utilizing the endocyclic torsion angles, are small and can be neglected. 31 The endocyclic torsion angles are useful in the calculation of the ring puckering parameters. They are utilized not only for describing the five-membered ring puckering, but also for the six-membered ring puckering.…”

Section: Theorymentioning

confidence: 99%

The puckering free-energy surface of proline

2013

AIP Advances

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Proline has two preferred puckering states, which are often characterized by the pseudorotation phase angle and amplitude. Although proline's five endocyclic torsion angles can be utilized to calculate the phase angle and amplitude, it is not clear if there is any direct correlation between each torsion angle and the proline-puckering pathway. Here we have designed five proline puckering pathways utilizing each torsion angle χj (j = 1∼5) as the reaction coordinate. By examining the free-energy surfaces of the five puckering pathways, we find they can be categorized into two groups. The χ2 pathway (χ2 is about the Cβ—Cγ bond) is especially meaningful in describing proline puckering: it changes linearly with the puckering amplitude and symmetrically with the phase angle. Our results show that this conclusion applies to both trans and cis proline conformations. We have also analyzed the correlations of proline puckering and its backbone torsion angles ϕ and ψ. We show proline has preferred puckering states at the specific regions of ϕ, ψ angles. Interestingly, the shapes of ψ-χ2 free-energy surfaces are similar among the trans proline in water, cis proline in water and cis proline in the gas phase, but they differ substantially from that of the trans proline in the gas phase. Our calculations are conducted using molecular simulations; we also verify our results using the proline conformations selected from the Protein Data Bank. In addition, we have compared our results with those calculated by the quantum mechanical methods

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“…To monitor the sugar pucker of target nucleotide, we used cpptraj. [69][70][71] Pocket volumes were studied using POVME3.0 [72][73][74] and visualized using Visual Molecular Dynamics. 75 The pocket region was defined by a set of inclusion spheres which cover the observed DNA binding region ( Figure S1).…”

Section: Methodsmentioning

confidence: 99%

Determinants of Substrate Specificity in APOBEC3B

Wagner

Demir²,

Carpenter³

et al. 2018

Preprint

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APOBEC3B (A3B) is a newly discovered driver of mutation in many cancers. We use computational tools to revert a recent crystal structure of an A3B construct to its native sequence, and run molecular dynamics simulations to study its underlying dynamics and substrate recognition mechanisms. The A3B oligonucleotide substrate simulations show a series of dynamic substrate protein contacts that correlate with previous work on A3B substrate selectivity. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose showed a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B beginning in the open state experience a rapid and consistent closure of the binding site, reaching a conformation incompatible with substrate binding. These simulations agree with previous experimental studies, and we report the atomistic details of these events to further therapeutic studies on A3B. IntroductionThe APOBEC3 (A3) family of cytidine deaminases is a recently discovered endogenous source of mutation in cancer. 1,2 Previously, A3 proteins were studied in the context of their interactions with viruses and efforts were undertaken to discover small molecules that modulate the mutational activities of the virally restrictive APOBEC3G enzyme. 3,4 Recent studies have linked cancer progression and recurrence to A3 activity. 5-9 A3 proteins have specific substrate sequence preferences, and analyses of some cancer genomes have shown an enrichment of A3 mutation signatures. [10][11][12][13][14][15] Recent evidence suggests that APOBEC3B (A3B) is an important driver of tumor progression in the A3 family. 16,17

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Ribose puckering: structure, dynamics, energetics, and the pseudorotation cycle

Cited by 112 publications

References 0 publications

DNA Structure: Alphabet Soup for the Cellular Soul

DNA Structure: Alphabet Soup for the Cellular Soul

The puckering free-energy surface of proline

Determinants of Substrate Specificity in APOBEC3B

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