(NB: Manuals and SOPs are under “Instrumentation“)
Surface Plasmon Resonance (SPR/Biacore)
- GE biacore site
- University of Utah Center for Biomolecular Interaction Analysis
- Merwe, PA: Surface Plasmon Resonance
- Reichert SPR blog (tips & tricks for data acquisition, analysis and troubleshooting)
- Use of SA chips
- Regeneration by multivariate cocktails, PMID: 10405611.
BioLayer Interferometry (BLI/Octet)
- ForteBio Octet platform, how it works and associated literature
- Application note 14 on kinetic assays (highly recommended introductory reading)
- Application note 19 – optimisation of an FcRn – IgG assay with biphasic dissociation
- Optimising kinetic assays – technical tip
- Biosensor selection guide
- Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects – useful reading with video links
- Biotinylation of protein for immobilisation on streptavidin sensors – technical note 28
- Regeneration of streptavidin sensors – technical note 14
- Long-term storage of biosensors – technical tip
- Amine coupling kit – technical note 27
- Kinetic assays using Ni-NTA biosensors – technical note 31
- 96-well plate template
Isothermal Titration Calorimetry (ITC)
- MicroCal (now owned by Malvern)
- Origin software
- SCORPIO database of ITC data from structurally-characterised complexes
- “Isothermal Titration Calorimetry of Protein-Protein interactions” review by Pierce, Raman and Nall. PMID: 10527727.
- Thermodynamic quantities for the ionization reactions of buffers (doi:10.1063/1.1416902)
- Enthalpy and heat capacity changes for dissociation of protonated buffers (Fukada and Takahashi, Proteins, 1998. PMID: 9779785)
- Tight binding studies via competition (Velazquez-Campoy et al., Arch Biochem Biophys, 2001. PMID: 11396919; Nature Protocols, 2006. PMID: 17406231)
- O’Brien R, Ladbury JE and Chowdry BZ (2000) Isothermal titration calorimetry of biomolecules. Chapter 10 in Protein-Ligand interactions: hydrodynamics and calorimetry Ed. Harding SE and Chowdry BZ, OUP.
- “Isothermal titration calorimetry of RNA” (also excellent on general methodology). Salim NN & Feig AL (2008) Methods, 47, 198-205. PMID: 18835447.
Circular Dichroism Spectrometry (CD)
- CD at Aviv Biomedical
- Dichroweb at Birkbeck, plus course notes
- Electromagnetic waves and circular dichroism: an animated tutorial – fantastic visual explanation of the CD phenomenon by András Szilágyi
- Analysis of circular dichroism data. Greenfield NJ. (2004) Methods Enzymol, 383, 282-317. PMID: 15063655.
- “Determining the CD spectrum of a protein” from Current Protocols in Protein Science
- CD as a function of temperature, in Nature Protocols, 2006. PMID: 17406506.
- Estimation of secondary structure by CD, in Nature Protocols, 2006. PMID: 17406547.
- “Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis”. Sreerama N, Venyaminov SY, Woody RW.(2000) Anal Biochem, 287, 243-51. PMID: 11112270.
- “Correcting the circular dichroism spectra of peptides for contributions of absorbing side chains”. Krittanai C, Johnson WC. (1997) Anal Biochem, 253, 57-64. PMID: 9356142.
Analytical Ultracentrifugation (AUC)
- SEDFIT and SEDPHAT at the NIH with latest software downloads
- GUSSI (for nice graphical output from SEDFIT and SEDPHAT)
- Nottingham Centre for Macromolecular Hydrodynamics
- Excellent instructional video: “Assembly, Loading, and Alignment of an Analytical Ultracentrifuge Sample Cell” at the Journal of Visualized Experiments
- Walter Stafford’s “Time to equilibrium” calculator (according to Williams et al., 1958)
- SEDNTERP is available in various flavours: Windows, Linux, OSX 10.7 (Lion), OSX Intel 32 bit, also here and here
- SVEDBERG and DCDT+ from John Philo
- University of Texas CAUMA (Ultrascan)
- Walter Stafford’s pages at the Boston Biomedical Research Institute, also SEDANAL
- BITC and CAMIS at the University of New Hampshire
- University of Mississippi AUC Facility
- Beckman Coulter AUC pages, also primers “Introduction to AUC” and “Self-Associating Systems”
- Tutorial review from Peter Schuck’s lab
- Schuck review on associating systems
- What is the frictional ratio?
- Converting S to S20,w
- “Modern Analytical Ultracentrifugation” Methods 2011 review. PMID: 21536133.
- Spin Analytical
- Chemical resistance tables (including epoxy/carbon centrepieces)
Dynamic Light Scattering (DLS)
- Zetasizer Nano S
- Zetasizer software download (free!)
- Malvern DLS terms explained (e.g. Z-average, polydispersity…)
- Minimum concentration considerations
- Malvern calculators explained (found within software, under “Tools”)
- Create custom reports (YouTube)
Dynamic Scanning Fluorimetry (DSF, “Thermofluor”)
- “The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability” in Nature Protocols, 2007. PMID: 17853878
- ε205 calculator
- Hydrodynamic modelling software (HYDRO suite) from José García de la Torre’s lab
- Invitrogen Fluorescence SpectraViewer
- Invitrogen Fluorescence Fundamentals
- BioRad fluorophore reference guide
- Center for Fluorescence Spectroscopy at the University of Maryland
- Phillips Lab at Caltech
- Alliance Protein Laboratories
- Chemistry of crosslinking at Thermo/Pierce
- Crosslinking reagents at Thermo/Pierce