Two way street – complementary methods

An introduction to the 2014 CCP4 Study Weekend.

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented.

In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF

The current version of the Cryobench in crystallo optical spectroscopy facility of the ESRF is presented. The diverse experiments that can be performed at the Cryobench are also reviewed.

Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data

The particular challenge of the analysis of optical absorption and Raman spectroscopic data measured from protein crystals and how the SLS-APE software toolbox supports scientists in dealing with such data is described.

Protein–ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI)

The biophysical characterization of protein–ligand interactions in solution using techniques such as thermal shift assay, or on surfaces using, for example, dual polarization interferometry, plays an increasingly important role in complementing crystal structure determinations.

The accurate assessment of small-angle X-ray scattering data

A set of quantitative techniques is suggested for assessing SAXS data quality. These are applied in the form of a script, SAXStats, to a test set of 27 proteins, showing that these techniques are more sensitive than manual assessment of data quality.

Uniqueness of models from small-angle scattering data: the impact of a hydration shell and complementary NMR restraints

The potentialities and limitations of biomacromolecular modelling of small-angle scattering data are reviewed and discussed with a focus on the impact of complementary NMR restraints and a hydration shell.

BioSAXS Sample Changer: a robotic sample changer for rapid and reliable high-throughput X-ray solution scattering experiments

A robotic sample changer for solution X-ray scattering experiments optimized for speed and to use the minimum amount of material has been developed. This system is now in routine use at three high-brilliance European synchrotron sites, each capable of several hundred measurements per day.

ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments

The ISPyB information-management system for crystallography has been adapted to include data from small-angle X-ray scattering of macromolecules in solution experiments.

Memprot: a program to model the detergent corona around a membrane protein based on SEC–SAXS data

Systematic SAXS simulations have been analysed over a wide range of parameters in order to better understand the detergent corona around a membrane protein.

Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

An acoustic high-throughput screening method is described for harvesting protein crystals and combining the protein crystals with chemicals such as a fragment library.

Experimental phasing for structure determination using membrane-protein crystals grown by the lipid cubic phase method

Very little information is available in the literature concerning the experimental heavy-atom phasing of membrane-protein structures where the crystals have been grown using the lipid cubic phase (in meso) method. In this paper, pre-labelling, co-crystallization, soaking, site-specific mercury binding to genetically engineered single-cysteine mutants and selenomethionine labelling as applied to an integral membrane kinase crystallized in meso are described. An assay to assess cysteine accessibility for mercury labelling of membrane proteins is introduced.

Collaborative Computational Project for Electron cryo-Microscopy

The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported.

A national facility for biological cryo-electron microscopy

This review provides a brief update on the use of cryo-electron microscopy for integrated structural biology, along with an overview of the plans for the UK national facility for electron microscopy being built at the Diamond synchrotron.

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions.

Structure calculation, refinement and validation using CcpNmr Analysis

This report describes the working of the program CcpNmr Analysis for both NMR chemical shift assignment and structure determination of biological macromolecules.

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented.