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Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase

2019 Nucleic Acids Research  
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

L. A. Lipscomb, M. E. Peek, M. L. Morningstar, S. M. Verghis, E. M. Miller, A. Rich, J. M. Essigmann, L. D. Williams
1995 Proceedings of the National Academy of Sciences of the United States of America  
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]

Timothy David Craggs, Marko Sustarsic, Anne Plochowietz, Majid Mosayebi, Hendrik Kaju, Andrew Cuthbert, Johannes Hohlbein, Laura Domicevica, Philip C Biggin, Jonathan P. K. Doye, Achillefs N. Kapanidis
2018 bioRxiv   pre-print
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

Renuka Kadirvelraj, Jeong-Yeh Yang, Justin H. Sanders, Lin Liu, Annapoorani Ramiah, Pradeep Kumar Prabhakar, Geert-Jan Boons, Zachary A. Wood, Kelley W. Moremen
2018 Proceedings of the National Academy of Sciences of the United States of America  
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

Barbara Imperiali, S. E. O'Connor, Tamara Hendrickson, Christine Kellenberger
1999 Pure and Applied Chemistry  
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]

Junyan Ma, Nabanita Saikia, Subash Godar, George L Hamilton, Feng Ding, Joshua Alper, Hugo Sanabria
2021 bioRxiv   pre-print
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

Hari Shroff, David Sivak, Jake J. Siegel, A.L. McEvoy, Merek Siu, Andrew Spakowitz, Phillip L. Geissler, Jan Liphardt
2008 Biophysical Journal  
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

Junyan Ma, Nabanita Saikia, Subash Godar, George L Hamilton, Feng Ding, Joshua Alper, Hugo Sanabria
2021 RNA: A publication of the RNA Society  
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

Mario Wriedt, Julian P. Sculley, Andrey A. Yakovenko, Yuguang Ma, Gregory J. Halder, Perla B. Balbuena, Hong-Cai Zhou
2012 Angewandte Chemie International Edition  
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

Thomas Christian, Lou Romano, David Rueda
2010 Biophysical Journal  
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

Sagnik Chakraborty, Peter J Steinbach, Debamita Paul, Hong Mu, Suse Broyde, Jung-Hyun Min, Anjum Ansari
2017 Nucleic Acids Research  
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

V. Voelter, N. Rufer, S. Reynard, G. Greub, R. Brookes, P. Guillaume, F. Grosjean, T. Fagerberg, O. Michelin, S. Rowland-Jones, C. Pinilla, S. Leyvraz (+2 others)
2008 International Immunology  
(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

Yue Hao, Elizabeth Pierce, Daniel Roe, Maho Morita, John A. McIntosh, Vinayak Agarwal, Thomas E. Cheatham, Eric W. Schmidt, Satish K. Nair
2016 Proceedings of the National Academy of Sciences of the United States of America  
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

Xinjian Yan, Thomas Hollis, Maria Svinth, Philip Day, Arthur F Monzingo, George W.A Milne, Jon D Robertus
1997 Journal of Molecular Biology  
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

Mario Wriedt, Julian P. Sculley, Andrey A. Yakovenko, Yuguang Ma, Gregory J. Halder, Perla B. Balbuena, Hong-Cai Zhou
2012 Angewandte Chemie  
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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