Greg Hura and colleagues developed and applied nanogold labels for DNA complexes with proteins examined by small angle X-ray scattering (SAXS) to follow DNA conformations acting in error detection by the mismatch repair (MMR) system in solution. This technique can examine short or long pieces of DNA and in most solution conditions, including those closest to cellular environments. This technique is expected to be useful for many biologically important systems involving DNA complexes and conformations. In this manuscript the authors reveal DNA bending followed by straightening by the repair protein MutS at the site of a mismatch as a suitable mechanism for error detection and signaling needed to avoid mutations and cancers and to control microbial stability and evolution in response to environmental stress.
Mismatch DNA bending by MutS and straightening in the presence of ATP. Contour plots of the distribution of DNA ends are visualized by placing the structural information from the crystal structure of MutS/DNA on the same scale as the distance and pop- ulation information from the P(Dij) distributions. The P(Dij) distributions from 71-bp DNA in the presence of MutS (left) and the presence of MutS and excess ATP (right) set contour levels. The widest part of the distribution is the width of the gold nanocrystal. DNA of the crystal structure has been ex- tended to 71 bp for the MutS/DNA complex and replaced by straight DNA for the ATP model.
For all the details please check out the full manuscript:
We are pleased to announce the 4th annual SIBYLS bioSAXS workshop.
Date: October 8-9, 2013 Location: Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA
The SIBYLS team will host a workshop with strong emphasis on experimental aspects of Small Angle X-ray Scattering techniques in structural biology. The two-day workshop will provide training on experimental techniques and software tutorial sessions primarily for biological SAXS studies. The latest advances in SAXS studies on biological systems will be reported and discussed by invited experts including our keynote speakers Prof. Peter Moore (Yale), Pau Bernando (CNRS France) and John Tainer (Scripps). Also planned are presentations on solution structure modeling techniques for proteins, RNA, DNA-protein complexes. The second day of the workshop will be dedicated for processing of workshop participant data previously collected at SIBYLS.
Participants will receive updates on current software dedicated to analyze SAXS for structural biology:
Enrollment is limited to 30 participants.
Several new crystal structures of the 70S ribosome in complex with EFG and non-hydrolyzable GTP analogs have revealed how the ribosome directionally translocates mRNA and the tRNAs through the A, P, and E sites and how specific features of EFG and ribosomal RNA act as pawls to enforce this ratcheting mechanism. The new structures were solved in the Cate, Noller, and Ramakrishnan labs and were published in the June 28 edition of Science. Many of the new structures were made possible by data collected at the SIBYLS beamline.
If you want the boiled down version of these new results then read this succinct comment by Marina Rodnina.
A figure liberally lifted from her comment.
We spent many long nights at the Advanced Light Source, running on coffee, donuts and barbecued ribs from the legendary Everett & Jones BBQ in West Berkeley.
A very interesting historical reflection by Harry Noller entitled “By Ribosome Possessed” has just been published in JBC. It is his personal account of growing up in the East Bay; his educational, musical, and scientific influences and how these gradually but inexorably led to an exciting and fruitful career studying “one of the deepest and most central mechanisms in all of biology”. The article is filled with funny and amazing anecdotes and gives a very human face to science, and to Harry’s impressively focused and singular pursuit of one of life’s most important molecules. A great read!
SIBYLS scientists have recently published and made available tools for generating SAXS structural comparison maps. Details of the methods have been published in Nature Methods.
Biological macromolecular functions require distinct conformational states that are challenging to examine comprehensively. Current methods to quantify conformational similarities and distinguish different assembly states are underdeveloped. Recent developments in small-angle X-ray scattering (SAXS) have shown that SAXS can provide the resolution to resolve conformational states, characterize flexible macromolecules and screen in high throughput under most solution conditions1. However, robust tools for comprehensively characterizing and visualizing the different conformational states identified by SAXS have been lacking. Here we present the SAXS structural comparison map (SCM) and volatility of ratio (VR) difference metric, which together provide quantitative and superposition-independent evaluation of solution-state conformations.
read more in the full article…
Rob and John have a new review on SAXS and its application to systems biology published in the Annual Review of Biophysics. See if you can spot the musical theme.
Small-angle X-ray scattering (SAXS) is a robust technique for the comprehensive structural characterizations of biological macromolecular complexes in solution. Here, we present a coherent synthesis of SAXS theory and experiment with a focus on analytical tools for accurate, objective, and high-throughput investigations. Perceived SAXS limitations are considered in light of its origins, and we present current methods that extend SAXS data analysis to the super-resolution regime. In particular, we discuss hybrid structural methods, illustrating the role of SAXS in structure refinement with NMR and ensemble refinement with single-molecule FRET. High-throughput genomics and proteomics are far outpacing macromolecular structure determinations, creating information gaps between the plethora of newly identified genes, known structures, and the structure-function relationship in the underlying biological networks. SAXS can bridge these information gaps by providing a reliable, high-throughput structural characterization of macromolecular complexes under physiological conditions.