Dr Timothy D. Craggs

Tim Craggs

Lecturer in Biological Chemistry
Department of Chemistry
The University of Sheffield
Brook Hill
Sheffield S3 7HF
United Kingdom

Telephone: +44 (0) 114 222 9347
Email: t.craggs@sheffield.ac.uk

Craggs Group Website

General	Biographical Sketch Dr Tim Craggs obtained his MSci in Chemistry from the University of Cambridge in 2002. After his PhD (Cambridge 2007) and a postdoc in St Andrews, he took up a Lindemann Fellowship at Yale University (2010), followed by senior postdoc positions at Oxford (Kapanidis Lab) and Bristol (Dillingham Lab). In 2016 he was appointed to a Lectureship in Chemical Biology at the University of Sheffield. Research Keywords Single Molecule Spectroscopy Teaching Interests Biological Chemistry
Research	Single-molecule approaches provide unprecedented detail to the understanding of essential biological processes, as was recognized in the awarding of the 2014 Nobel Prize for Chemistry. Their unique advantage stems from the ability to go beyond the ensemble- and time-averaging of common biochemical techniques, enabling the identification and interpretation of asynchronous reactions, transient states, and rare sub-species. Research in the Craggs Lab involves the development and application of single-molecule fluorescence techniques to addressing crucial questions across physics, chemistry and the life sciences. Recent work has focussed on the development and application of single-molecule fluorescence resonance energy transfer (smFRET – a molecular ruler for the 30-90 Å scale) to questions of protein folding, and DNA transcription, replication and repair. These methods are capable of observing individual molecules and molecular interactions in real time, and understanding their dynamics. In addition to this mechanistic work, we have shown we can use smFRET to measure absolute distances with angstrom accuracy, opening the door to FRET driven structural biology.
Teaching	Undergraduate and postgraduate taught modules An Introduction to Biology for Physical Scientists (Level 1) This unit provides a basic knowledge and understanding of the occurrence, structure and function of important types of biopolymers such as proteins and nucleic acids, their organisation into biomaterials and their function in living systems. Biopolymers and Biomaterials (Post-graduate Level) This course explores the occurrence, structure and function of important types of biopolymers such as proteins and nucleic acids, their organisation into biomaterials and their function in living systems. Support Teaching: Level 3 Literature Review Laboratory Teaching: Level 2 Organic Laboratories Level 3 Research Project Level 4 Research Project

General

Biographical Sketch

Dr Tim Craggs obtained his MSci in Chemistry from the University of Cambridge in 2002. After his PhD (Cambridge 2007) and a postdoc in St Andrews, he took up a Lindemann Fellowship at Yale University (2010), followed by senior postdoc positions at Oxford (Kapanidis Lab) and Bristol (Dillingham Lab). In 2016 he was appointed to a Lectureship in Chemical Biology at the University of Sheffield.

Research Keywords

Single Molecule Spectroscopy

Teaching Interests

Biological Chemistry

Research

Single-molecule approaches provide unprecedented detail to the understanding of essential biological processes, as was recognized in the awarding of the 2014 Nobel Prize for Chemistry. Their unique advantage stems from the ability to go beyond the ensemble- and time-averaging of common biochemical techniques, enabling the identification and interpretation of asynchronous reactions, transient states, and rare sub-species.

Research in the Craggs Lab involves the development and application of single-molecule fluorescence techniques to addressing crucial questions across physics, chemistry and the life sciences.

Recent work has focussed on the development and application of single-molecule fluorescence resonance energy transfer (smFRET – a molecular ruler for the 30-90 Å scale) to questions of protein folding, and DNA transcription, replication and repair. These methods are capable of observing individual molecules and molecular interactions in real time, and understanding their dynamics.

In addition to this mechanistic work, we have shown we can use smFRET to measure absolute distances with angstrom accuracy, opening the door to FRET driven structural biology.

Teaching

Undergraduate and postgraduate taught modules

An Introduction to Biology for Physical Scientists (Level 1)
This unit provides a basic knowledge and understanding of the occurrence, structure and function of important types of biopolymers such as proteins and nucleic acids, their organisation into biomaterials and their function in living systems.
Biopolymers and Biomaterials (Post-graduate Level)
This course explores the occurrence, structure and function of important types of biopolymers such as proteins and nucleic acids, their organisation into biomaterials and their function in living systems.

Support Teaching:

Level 3 Literature Review

Laboratory Teaching:

Level 2 Organic Laboratories
Level 3 Research Project
Level 4 Research Project

Publications

Journal articles

Craggs TD, Sustarsic M, Plochowietz A, Mosayebi M, Kaju H, Cuthbert A, Hohlbein J, Domicevica L, Biggin PC, Doye JPK & Kapanidis AN (2019) Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. Nucleic Acids Research, 47(20), 10788-10800.
Martin E, Williams HEL, Pitoulias M, Stevens D, Winterhalter C, Craggs TD, Murray H, Searle MS & Soultanas P (2019) DNA replication initiation in Bacillus subtilis: structural and functional characterization of the essential DnaA–DnaD interaction. Nucleic Acids Research, 47(4), 2101-2112.
Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Adariani SR, Ambrose B, Aznauryan M, Barth A, Birkedal V , Bowen ME et al (2018) Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nature Methods, 15(9), 669-676. View this article in WRRO
Bennet I, Finger LD, Baxter NJ, Ambrose B, Hounslow A, Thompson MJ, Exell JC, Shahari NNBM, Craggs TD, Waltho JP & Grasby JA (2018) Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1. Nucleic Acids Research, 46(11), 5618-5633. View this article in WRRO
Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Adariani SR, Ambrose B, Aznauryan M, Barth A, Birkedal V , Bowen ME et al (2018) Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nature Methods, 15(11), 984-984.
Fisher GLM, Pastrana CL, Higman VA, Koh A, Taylor JA, Butterer A, Craggs TD, Sobott F, Murray H, Crump MP , Moreno-Herrero F et al (2017) The structural basis for dynamic DNA binding and bridging interactions which condense the bacterial centromere. eLife, 6. View this article in WRRO
Craggs TD (2017) Cool and dynamic: single-molecule fluorescence-based structural biology. Nature Methods, 14(2), 123-124.
Meli M, Sustarsic M, Craggs TD, Kapanidis AN & Colombo G (2016) DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations. Frontiers in Molecular Biosciences, 3. View this article in WRRO
Nott TJ, Craggs TD & Baldwin AJ (2016) Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters. Nature Chemistry, 8(6), 569-575.
Algasaier SI, Exell JC, Bennet IA, Thompson MJ, Gotham VJB, Shaw SJ, Craggs TD, Finger LD & Grasby JA (2016) DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction. Journal of Biological Chemistry, 291(15), 8258-8268. View this article in WRRO
Evans GW, Hohlbein J, Craggs T, Aigrain L & Kapanidis AN (2015) Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms. Nucleic Acids Research, 43(12), 5998-6008.
Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD & Baldwin AJ (2015) Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles. Molecular Cell, 57(5), 936-947.
Blouin S, Craggs TD, Lafontaine DA & Penedo JC (2015) Functional Studies of DNA-Protein Interactions Using FRET Techniques, 115-141.
(2014) Additions and corrections published 30th October 2013 to 15th July 2014. Chemical Society Reviews, 43(17), 6470-6470.
Craggs TD, Hutton RD, Brenlla A, White MF & Penedo JC (2014) Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Research, 42(3), 1857-1872. View this article in WRRO
Craggs TD, Sustarsic M, Hohlbein J, Cuthbert A, Taylor N, Evans G & Kapanidis AN (2014) A Novel FRET-Based Structure of DNA Polymerase Complexed with Kinked Gapped-DNA. Biophysical Journal, 106(2), 274a-274a.
Hohlbein J, Craggs TD & Cordes T (2014) Alternating-laser excitation: single-molecule FRET and beyond (vol 43, pg 1156, 2014). CHEMICAL SOCIETY REVIEWS, 43(17), 6472-6472.
Robb NC, Cordes T, Hwang LC, Gryte K, Duchi D, Craggs TD, Santoso Y, Weiss S, Ebright RH & Kapanidis AN (2013) The Transcription Bubble of the RNA Polymerase–Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection. Journal of Molecular Biology, 425(5), 875-885.
Hohlbein J, Aigrain L, Craggs TD, Bermek O, Potapova O, Shoolizadeh P, Grindley NDF, Joyce CM & Kapanidis AN (2013) Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nature Communications, 4(1). View this article in WRRO
Craggs TD & Kapanidis AN (2012) Six steps closer to FRET-driven structural biology. Nature Methods, 9(12), 1157-1158.
Hutton RD, Craggs TD, White MF & Penedo JC (2010) PCNA and XPF cooperate to distort DNA substrates. Nucleic Acids Research, 38(5), 1664-1675. View this article in WRRO
Craggs TD (2010) ChemInform Abstract: Green Fluorescent Protein: Structure, Folding and Chromophore Maturation. ChemInform, 41(3).
Craggs TD (2009) Green fluorescent protein: structure, folding and chromophore maturation. Chemical Society Reviews, 38(10), 2865-2865.
Blouin S, Craggs TD, Lafontaine DA & Penedo JC (2009) Functional Studies of DNA-Protein Interactions Using FRET Techniques, 475-502.
Orte A, Craggs TD, White SS, Jackson SE & Klenerman D (2008) Evidence of an Intermediate and Parallel Pathways in Protein Unfolding from Single-Molecule Fluorescence. Journal of the American Chemical Society, 130(25), 7898-7907.
Kuprov I, Craggs TD, Jackson SE & Hore PJ (2007) Spin Relaxation Effects in Photochemically Induced Dynamic Nuclear Polarization Spectroscopy of Nuclei with Strongly Anisotropic Hyperfine Couplings. Journal of the American Chemical Society, 129(29), 9004-9013.
Huang J-R, Craggs TD, Christodoulou J & Jackson SE (2007) Stable Intermediate States and High Energy Barriers in the Unfolding of GFP. Journal of Molecular Biology, 370(2), 356-371.
Jackson SE, Craggs TD & Huang J-R (2006) Understanding the folding of GFP using biophysical techniques. Expert Review of Proteomics, 3(5), 545-559.
Khan F, Kuprov I, Craggs TD, Hore PJ & Jackson SE (2006) 19F NMR Studies of the Native and Denatured States of Green Fluorescent Protein. Journal of the American Chemical Society, 128(33), 10729-10737.
Craggs TD, Sustarsic M, Plochowietz A, Mosayebi M, Kaju H, Cuthbert A, Hohlbein J, Domicevica L, Biggin PC, Doye JPK & Kapanidis AN () Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase.
Hohlbein J, Craggs TD & Cordes T () Alternating-laser excitation: single-molecule FRET and beyond. Chem. Soc. Rev., 43(4), 1156-1171.

Conference proceedings papers

Fisher GLM, Bateman BC, Craggs TD & Dillingham MS (2018) The Conformational Landscape of SMC: A FRET Study. Biophysical Journal, Vol. 114(3) (pp 209a-209a)
Craggs TD, Sustarsic M, Mosayebi M, Kaju H, Hohlbein J, Biggin PC, Doye JPK & Kapanidis AN (2016) How Structure-Specific DNA-Binding Proteins Recognise their Substrates. Biophysical Journal, Vol. 110(3) (pp 514a-515a)
Craggs TD, Sustarsic M, Hohlbein J, Cuthbert A, Taylor N, Evans G & Kapanidis AN (2014) A Novel FRET-Based Structure of DNA Polymerase Complexed with Kinked Gapped-DNA. BIOPHYSICAL JOURNAL, Vol. 106(2) (pp 273A-273A)
Orte A, Craggs TD, White SS, Jackson SE & Klenerman D (2007) YFP unfolding kinetics studied in a single-molecule nano-flow cell. BIOPHYSICAL JOURNAL (pp 660A-660A)

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