Substrate-Dependent Millisecond Domain Motions in DNA Polymerase β

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Journal of Molecular Biology (Impact Factor: 4.33). 03/2012; 419(3-4):171-82. DOI: 10.1016/j.jmb.2012.03.013
Source: PubMed


DNA polymerase β (Pol β) is a 39-kDa enzyme that performs the vital cellular function of repairing damaged DNA. Mutations in Pol β have been linked to various cancers, and these mutations are further correlated with altered Pol β enzymatic activity. The fidelity of correct nucleotide incorporation into damaged DNA is essential for Pol β repair function, and several studies have implicated conformational changes in Pol β as a determinant of this repair fidelity. In this work, the rate constants for domain motions in Pol β have been determined by solution NMR relaxation dispersion for the apo and substrate-bound, binary forms of Pol β. In apo Pol β, molecular motions, primarily isolated to the DNA lyase domain, are observed to occur at 1400 s(-1). Additional analysis suggests that these motions allow apo Pol β to sample a conformation similar to the gapped DNA-substrate-bound form. Upon binding DNA, these lyase domain motions are significantly quenched, whereas evidence for conformational motions in the polymerase domain becomes apparent. These NMR studies suggest an alteration in the dynamic landscape of Pol β due to substrate binding. Moreover, a number of the flexible residues identified in this work are also the location of residues, which upon mutation lead to cancer phenotypes in vivo, which may be due to the intimate role of protein motions in Pol β fidelity.

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    • "It is possible that the high flexibility of L1 of p53 DBD plays an important role in this process of tread-milling (Figure 8). Another study on DNA polymerase β shows that its lyase domain is flexible in the DNA-free state, but is dominantly quenched in its motions when bound to DNA [85]. On the other hand, its polymerase domain is less flexible in the DNA-bound state than in the free state. "
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    ABSTRACT: The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD). In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs). Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3). Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart). Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1) a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2) possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.
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    ABSTRACT: Incorporating the cognate instead of non-cognate substrates is crucial for DNA polymerase function. Here we analyze molecular dynamics simulations of DNA polymerase μ (pol μ) bound to different non-cognate incoming nucleotides including A:dCTP, A:dGTP, A(syn):dGTP, A:dATP, A(syn):dATP, T:dCTP, and T:dGTP to study the structure-function relationships involved with aberrant base pairs in the conformational pathway; while a pol μ complex with the A:dTTP base pair is available, no solved non-cognate structures are available. We observe distinct differences of the non-cognate systems compared to the cognate system. Specifically, the motions of active-site residue His329 and Asp330 distort the active site, and Trp436, Gln440, Glu443 and Arg444 tend to tighten the nucleotide-binding pocket when non-cognate nucleotides are bound; the latter effect may further lead to an altered electrostatic potential within the active site. That most of these "gate-keeper" residues are located farther apart from the upstream primer in pol μ, compared to other X family members, also suggests an interesting relation to pol μ's ability to incorporate nucleotides when the upstream primer is not paired. By examining the correlated motions within pol μ complexes, we also observe different patterns of correlations between non-cognate systems and the cognate system, especially decreased interactions between the incoming nucleotides and the nucleotide-binding pocket. Altered correlated motions in non-cognate systems agree with our recently proposed hybrid conformational selection/induced-fit models. Taken together, our studies propose the following order for difficulty of non-cognate system insertions by pol μ: T:dGTP<A(syn):dATP<T:dCTP<A:dGTP<A(syn):dGTP<A:dCTP<A:dATP. This sequence agrees with available kinetic data for non-cognate nucleotide insertions, with the exception of A:dGTP, which may be more sensitive to the template sequence. The structures and conformational aspects predicted here are experimentally testable.
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    ABSTRACT: Domain dynamics in biomacromolecules is currently an area of intense research because of its importance for understanding the huge quantity of available data relating the structure and function of proteins and nucleic acids. Control of structural flexibility is essential for the proper functioning of the biomacromolecules. Biophysical discoveries as well as computational algorithms and databases have reshaped our understanding of the often spectacular domain dynamics. At the residue level, such flexibility occurs due to local relaxation of peptide bond angles whose cumulative effect results in large changes in the secondary, tertiary or quaternary structures. The flexibility, or its absence, most often depends on the nature of interdomain linkages. Both the flexible and relatively rigid linkers are found in many multidomain biomacromolecules. Large-scale structural heterogeneity of multidomain biomacromolecules and their complexes is now seen as the norm rather than the exception. Absence of such motion, as in the so-called molecular rulers, also has desirable functional effects in architecture of biomacromolecules. The contemporary methods of NMR spectroscopy are capable to provide the detailed information on domain motions in biomacromolecules in the wide range of timescales related to the timescales of their functioning. We review here the current point of view on the nature of domain motions based on these last achievements in the field of NMR spectroscopy. Experimental and theoretical aspects of the collective intra- and interdomain motions are considered.
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Rebecca Beth Berlow