X-ray crystallography, cryo-EM, NMR, AlphaFold, protein-structure determination pipelines.
Structural Biology Methods
X-ray crystallography
Determines atomic structure from X-ray diffraction by protein crystal. Phase problem solved by MR, MAD, SAD, direct methods. Resolution:…
Cryo-electron microscopy
Single-particle electron microscopy of vitrified specimens. 'Resolution revolution' (2013): direct electron detectors + 3D reconstruction…
Protein NMR spectroscopy
Protein structure determination from chemical-shift + NOE + RDC restraints. Size limit ~40-50 kDa; unique for dynamics (μs-ms motions,…
AlphaFold
DeepMind 2020/2021 neural-network protein-structure predictor. CASP14 breakthrough; AF2 achieves experimental accuracy on most domains…
Mass spectrometry proteomics
Peptide identification + quantification by MS/MS. Bottom-up (tryptic digest) most common. Workflows: LC-MS/MS → database search (Mascot,…
Biomolecular molecular dynamics
Newtonian integration of atomic motions using force fields (AMBER, CHARMM, GROMOS). Timescales: μs-ms with enhanced sampling (REMD,…
Size-exclusion chromatography + PDB
Protein preparation: express → purify (Ni-NTA, SEC, IEC) → biophysical QC (DLS, CD, SEC-MALS). Structures deposited in Protein Data Bank…
Small-angle X-ray scattering (SAXS)
Solution-scattering technique reporting low-resolution shape + oligomeric state. Pair-distance distribution function P(r), Rg, molecular…
Single-molecule FRET
FRET between donor-acceptor fluorophores on single molecule reveals conformational dynamics. Distance range 2-10 nm. Reveals…
Hydrogen-deuterium exchange MS
Backbone amide H → D exchange rate probes solvent accessibility + dynamics. HDX-MS maps protein-ligand interfaces, allosteric changes,…