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G1/S Transcription Factor Copy Number Is a Growth-Dependent Determinant of Cell Cycle Commitment in Yeast. Cell Syst 2018; 6:539-554.e11. [DOI: 10.1016/j.cels.2018.04.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/17/2018] [Accepted: 04/25/2018] [Indexed: 11/20/2022]
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Liu J, Huang J, Zhao Y, Liu H, Wang D, Yang J, Zhao W, Taylor IA, Peng YL. Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains. Nucleic Acids Res 2014; 43:1231-40. [PMID: 25550425 PMCID: PMC4333399 DOI: 10.1093/nar/gku1351] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The MBP1 family proteins are the DNA binding subunits of MBF cell-cycle transcription factor complexes and contain an N terminal winged helix-turn-helix (wHTH) DNA binding domain (DBD). Although the DNA binding mechanism of MBP1 from Saccharomyces cerevisiae has been extensively studied, the structural framework and the DNA binding mode of other MBP1 family proteins remains to be disclosed. Here, we determined the crystal structure of the DBD of PCG2, the Magnaporthe oryzae orthologue of MBP1, bound to MCB-DNA. The structure revealed that the wing, the 20-loop, helix A and helix B in PCG2-DBD are important elements for DNA binding. Unlike previously characterized wHTH proteins, PCG2-DBD utilizes the wing and helix-B to bind the minor groove and the major groove of the MCB-DNA whilst the 20-loop and helix A interact non-specifically with DNA. Notably, two glutamines Q89 and Q82 within the wing were found to recognize the MCB core CGCG sequence through making hydrogen bond interactions. Further in vitro assays confirmed essential roles of Q89 and Q82 in the DNA binding. These data together indicate that the MBP1 homologue PCG2 employs an unusual mode of binding to target DNA and demonstrate the versatility of wHTH domains.
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Affiliation(s)
- Junfeng Liu
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Jinguang Huang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yanxiang Zhao
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Huaian Liu
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Dawei Wang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Wensheng Zhao
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Ian A Taylor
- Division of Molecular Structure, MRC-NIMR, London, NW7 1AA, UK
| | - You-Liang Peng
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
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Sinha SK, Bandyopadhyay S. Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations. J Chem Phys 2012; 135:135101. [PMID: 21992339 DOI: 10.1063/1.3634004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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Chernatynskaya AV, Deleeuw L, Trent JO, Brown T, Lane AN. Structural analysis of the DNA target site and its interaction with Mbp1. Org Biomol Chem 2009; 7:4981-91. [PMID: 19907790 DOI: 10.1039/b912309a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solution structure of a 14 base-pair non-self complementary DNA duplex containing the consensus-binding site of the yeast transcription factor Mbp1 has been determined by NMR using a combination of scalar coupling analysis, time-dependent NOEs, residual dipolar couplings and 13C-edited NMR spectroscopy of a duplex prepared with one strand uniformly labeled with 13C-nucleotides. As expected, the free DNA duplex is within the B-family of structures, and within experimental limits is straight. However, there are clear local structural variations associated with the consensus CGCG element in the binding sequence that are important for sequence recognition. In the complex, the DNA bends around the protein, which also undergoes some conformational rearrangement in the C-terminal region. Structural constraints derived from paramagnetic perturbation experiments with spin-labeled DNA, chemical shift perturbation experiments of the DNA, previous cross-saturation, chemical shift perturbation experiments on the protein, information from mutational analysis, and electrostatics calculations have been used to produce a detailed docked structure using the known solution conformation of the free protein and other spectroscopic information about the Mbp1:DNA complex. A Monte Carlo-based docking procedure with restrained MD in a fully solvated system subjected to available experimental constraints produced models that account for the available structural data, and can rationalize the extensive thermodynamic data about the Mbp1:DNA complex. The protein:DNA interface is closely packed and is associated with a small number of specific contacts. The structure shows an extensive positively charged surface that accounts for the high polyelectrolyte contribution to binding.
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Eliseo T, Sánchez IE, Nadra AD, Dellarole M, Paci M, de Prat Gay G, Cicero DO. Indirect DNA Readout on the Protein Side: Coupling between Histidine Protonation, Global Structural Cooperativity, Dynamics, and DNA Binding of the Human Papillomavirus Type 16 E2C Domain. J Mol Biol 2009; 388:327-44. [PMID: 19285507 DOI: 10.1016/j.jmb.2009.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 03/06/2009] [Accepted: 03/06/2009] [Indexed: 11/26/2022]
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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