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Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase
2019
Nucleic Acids Research
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Using a docking approach based on a network of 73 distances collected using single-molecule FRET, we determined a novel solution structure of the single-nucleotide-gapped DNA-Pol binary complex. ...
MD simulations and single-molecule assays also revealed that 4-5 nt of downstream gap-proximal DNA are unwound in the binary complex. ...
ACKNOWLEDGEMENTS We thank Maria Musgaard for assistance with all-atom MD simulations, and Nicholas Taylor for initial protein-DNA smFRET measurements. ...
doi:10.1093/nar/gkz797
pmid:31544938
pmcid:PMC6846080
fatcat:ywj46n35dngqlo3zni32hqizay
X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine
1995
Proceedings of the National Academy of Sciences of the United States of America
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The results demonstrate that Go forms Watson-Crick base pairs with the opposite C and that Go Abbreviations: Go, 7,8-dihydro-8-oxoguanine. §Present address: ...
Simulated annealing (XPLOR) decreased the R factor to 29.1%. The moderate decrease in R factor upon Proc. Natt Acad Sci USA 92 (1995) simulated annealing reflects the accuracy of the starting model. ...
We propose that hydrogen bonding properties of certain covalently modified purines provide a common recognition element among MutM substrates. MATERIALS AND METHODS DNA Synthesis. ...
doi:10.1073/pnas.92.3.719
pmid:7846041
pmcid:PMC42691
fatcat:6sy7u3gejzafjind64xoxbk52u
Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase
[article]
2018
bioRxiv
pre-print
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Coarse-grained simulations on free gapped substrates reproduced our experimental FRET values with remarkable accuracy (<ΔFRET> = -0.0025 across 34 independent distances) and revealed that the one-nucleotide-gapped ...
Using a rigid-body docking approach based on a network of 73 distance restraints collected using single-molecule FRET, we determined a novel solution structure of the singlenucleotide-gapped DNA-Pol binary ...
DNA labelling and annealing. ...
doi:10.1101/263038
fatcat:bhrdieghuvabhozukpqystbhxm
HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite
2018
Proceedings of the National Academy of Sciences of the United States of America
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The enzymatic steps required for the synthesis of these complex-type structures follow a discrete hierarchy based on the substrate specificities of the respective enzymes. ...
Structures of MGAT2-substrate complexes reveal both modular and convergent mechanisms for selective substrate recognition and catalysis and provide a generalized model for template-based synthesis of glycan ...
We thank Bobby Ng and Hudson Freeze for providing information on CDG IIa patient mutations. This research was supported by NIH Grants P41GM103390 and P01GM107012 (to K.W.M., G.-J.B., and Z.A.W.). ...
doi:10.1073/pnas.1716988115
pmid:29666272
fatcat:hvw3dkptpjdo7m2wgyu62qbvwa
Chemistry and biology of asparagine-linked glycosylation
1999
Pure and Applied Chemistry
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Recent research on the chemistry and biology of asparagine-linked glycosylation in our group has been focused on two speci®c areas. ...
Glycopeptide synthesis was effected using a modi®cation of the methods developed previously [23, 24] . ...
] on the glycine adjacent to the aspartic acid during the peptide synthesis. ...
doi:10.1351/pac199971050777
fatcat:prkvaq2xkreendgm4gpnzjqi7e
Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch
[article]
2021
bioRxiv
pre-print
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Moreover, we propose that two pathways exist for ligand recognition. ...
Thiamine pyrophosphate (TPP) riboswitches regulate thiamine metabolism by inhibiting the translation of enzymes essential to thiamine synthesis pathways upon binding to thiamine pyrophosphate in cells ...
Previous work on TPP riboswitches has focused on the TPP ligand recognition process. ...
doi:10.1101/2021.03.12.434875
fatcat:gqqgbvlpabb2jeitlgcgj3gipe
Optical Measurement of Mechanical Forces Inside Short DNA Loops
2008
Biophysical Journal
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Monte Carlo simulations based on the helical wormlike chain model accurately predict internal forces when more than half of the loop is dsDNA but fail otherwise. ...
Knowledge of the mechanical properties of double-stranded DNA (dsDNA) is essential to understand the role of dsDNA looping in gene regulation and the mechanochemistry of molecular machines that operate on ...
MATERIALS AND METHODS
Synthesis, purification, and annealing of loop constructs Dual-fluorophore labeled oligonucleotides of lengths 57, 81, and 101 bases (sequences given in the Supplementary Material ...
doi:10.1529/biophysj.107.114413
pmid:18065484
pmcid:PMC2257878
fatcat:dcrvmyeaanbcxovv3vjmktextq
Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch
2021
RNA: A publication of the RNA Society
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Thiamine pyrophosphate (TPP) riboswitches regulate thiamine metabolism by inhibiting the translation of enzymes essential to thiamine synthesis pathways upon binding to thiamine pyrophosphate in cells ...
of TPP recognition and subsequent transition to the expression-inhibiting state of the aptamer domain followed by changes in the expression platform. ...
Gerd Kotzorek of Purimex for his assistance in synthesis, purifying, and labeling the riboswitch aptamer domain. This work was sup- Received April 21, 2020; accepted April 13, 2021. ...
doi:10.1261/rna.075937.120
pmid:33863818
fatcat:izva5km5gzg6bp3hceb62egrou
Low-Energy Selective Capture of Carbon Dioxide by a Pre-designed Elastic Single-Molecule Trap
2012
Angewandte Chemie International Edition
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We established this elastic CO 2 trapping effect of PCN-200 using four independent methods: single-component gas-adsorption isotherms, binary gas adsorption studies by simulations and experiments, and ...
The resulting multipoint bonding of CO 2 to a precisely designed pocket is reminiscent of the biomimetic recognition employed by receptors in nature to accommodate exactly one guest molecule. ...
Based on the simulations, crystal structure and adsorption data, we can exclude molecular sieving as a possible mechanism for the selectivity. ...
doi:10.1002/anie.201202992
pmid:22945893
fatcat:ddafi7pykbhvjajqtwycnjsmhi
Single-Molecule Measurements of Synthesis by DNA Polymerase with Base-Pair Resolution
2010
Biophysical Journal
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Using DNA polymerase I (Klenow fragment) labeled with both donor and acceptor fluorophores, we have employed single-molecule fluorescence resonance energy transfer (smFRET) to study the polymerase conformational ...
One scenario is that the two sister MCM2-7 complexes dissociate during initiation and then travel away from one another. Alternatively, the sister helicases might remain physically coupled. ...
To further understand the energetics of base flipping in MutS, we utilized the Hamiltonian replica-exchange molecular dynamics (HREMD) method simulating 44 independent replicas in an explicit water box ...
doi:10.1016/j.bpj.2009.12.2375
fatcat:urkam6ysn5f6fckycy32cdcque
Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex
2017
Nucleic Acids Research
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Molecular dynamics simulations also revealed a wide distribution of conformations for CCC/CCC, complementing experimental findings. ...
However, characterizing how DNA deformability and/or distortions impact recognition has been challenging. ...
The FRET values between tC • and tC nitro , obtained as described in Supplementary Methods 1.7-1.9, were compared with theoretical predictions based on DNA structures, as described in Supplementary Methods ...
doi:10.1093/nar/gkx1216
pmid:29267981
pmcid:PMC5815138
fatcat:6znfokbwvng2nfsdxkg57zmwlm
Characterization of Melan-A reactive memory CD8+ T cells in a healthy donor
2008
International Immunology
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(San Diego, CA, USA) by the simultaneous multiple peptide synthesis method. ...
The conformational sampling was performed using a simulated annealing protocol in which 1000 heating-cooling cycles were completed. ...
doi:10.1093/intimm/dxn066
pmid:18573812
fatcat:5x6rspgqb5fszoorfdghcs5xpu
Molecular basis for the broad substrate selectivity of a peptide prenyltransferase
2016
Proceedings of the National Academy of Sciences of the United States of America
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The cyanobactin prenyltransferases catalyze a series of known or unprecedented reactions on millions of different substrates, with no easily observable recognition motif and exquisite regioselectivity. ...
We determined the structures of the Tyr-prenylating enzyme PagF, in complex with an isoprenoid donor analog and a panel of linear and macrocyclic peptide substrates. ...
We thank Greg Bulaj for stimulating discussions, Scott Endicott for cyclic peptide synthesis, Amy Barrios and Elena Shuangyu Ma for use of the Aapptek peptide synthesizer and help with linear peptide synthesis ...
doi:10.1073/pnas.1609869113
pmid:27872314
pmcid:PMC5150373
fatcat:wi6kb6rgzbapnlkajvhinuw74m
Structure-based identification of a ricin inhibitor 1 1Edited by R. Huber
1997
Journal of Molecular Biology
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In this study computer-assisted searches indicated that pterins might bind in the RTA active site which normally recognizes a speci®c adenine base on rRNA. ...
The benzoate moiety of pteroic acid binds on the opposite side of Tyr80 making van der Waals contact with the Tyr ring and forming a hydrogen bond with Asn78. ...
, while the constant function simulates the solvent effect on the protein. ...
doi:10.1006/jmbi.1996.0865
pmid:9086280
fatcat:bdwemsii6vgtjczxrcot6mssgq
Low-Energy Selective Capture of Carbon Dioxide by a Pre-designed Elastic Single-Molecule Trap
2012
Angewandte Chemie
Preserved Fulltext
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Based on the simulations, crystal structure and adsorption data, we can exclude molecular sieving as a possible mechanism for the selectivity. ...
Recent investigations of compounds based on the same tzc ligand with similar N-donor ligands 4,4'-bipyridine [9] and 1,2-di(4-pyridyl)ethane [10] are nonporous; in the latter case, the tzc layer intersheet ...
doi:10.1002/ange.201202992
fatcat:hign7mh4c5fdlfxniggft7z3ym
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