Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

Download Full-text

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004714013856 ◽

2014 ◽

Vol 70 (9) ◽

pp. 2344-2355 ◽

Cited By ~ 33

Author(s):

Ryan McGreevy ◽

Abhishek Singharoy ◽

Qufei Li ◽

Jingfen Zhang ◽

Dong Xu ◽

...

Keyword(s):

Molecular Dynamics ◽

Large Scale ◽

Protein Structures ◽

Data Bank ◽

Real Space ◽

Low Resolution ◽

X Ray ◽

X Ray Crystallography ◽

Atomic Structures ◽

Electron Density Map

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally,viasystematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Download Full-text

Anomalies in the refinement of isoleucine

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s139900471400087x ◽

2014 ◽

Vol 70 (4) ◽

pp. 1037-1049 ◽

Cited By ~ 3

Author(s):

Karen R. M. Berntsen ◽

Gert Vriend

Keyword(s):

Molecular Dynamics ◽

High Resolution ◽

Secondary Structure ◽

Protein Structures ◽

Side Chain ◽

Energy Functions ◽

Torsion Angles ◽

X Ray ◽

X Ray Crystallography ◽

Target Values

A study of isoleucines in protein structures solved using X-ray crystallography revealed a series of systematic trends for the two side-chain torsion angles χ1and χ2dependent on the resolution, secondary structure and refinement software used. The average torsion angles for the nine rotamers were similar in high-resolution structures solved using either theREFMAC,CNSorPHENIXsoftware. However, at low resolution these programs often refine towards somewhat different χ1and χ2values. Small systematic differences can be observed between refinement software that uses molecular dynamics-type energy terms (for exampleCNS) and software that does not use these terms (for exampleREFMAC). Detailing the standard torsion angles used in refinement software can improve the refinement of protein structures. The target values in the molecular dynamics-type energy functions can also be improved.

Download Full-text

Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.10496 ◽

2003 ◽

Vol 53 (1) ◽

pp. 111-120 ◽

Cited By ~ 35

Author(s):

Hao Fan ◽

Alan E. Mark

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Nmr Spectroscopy ◽

Simulation Study ◽

Relative Stability ◽

Protein Structures ◽

Dynamics Simulation ◽

X Ray ◽

X Ray Crystallography

Download Full-text

Membrane protein crystallography in the era of modern structural biology

Biochemical Society Transactions ◽

10.1042/bst20200066 ◽

2020 ◽

Vol 48 (6) ◽

pp. 2505-2524

Author(s):

Tristan O. C. Kwan ◽

Danny Axford ◽

Isabel Moraes

Keyword(s):

Structural Biology ◽

Molecular Level ◽

Protein Structures ◽

Three Dimensional ◽

Biological Macromolecules ◽

X Ray ◽

X Ray Crystallography ◽

Cellular Processes ◽

Biochemical Level

The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.

Download Full-text