scholarly journals Structure determination of GPCRs: cryo-EM compared with X-ray crystallography

2021 ◽  
Author(s):  
Javier García-Nafría ◽  
Christopher G. Tate
Keyword(s):  
Structural Biology ◽  
Structure Determination ◽  
Drug Targets ◽  
Cellular Systems ◽  
Single Family ◽  
Structure Based Drug Design ◽  
X Ray ◽  
Surface Receptors ◽  
X Ray Crystallography

G protein-coupled receptors (GPCRs) are the largest single family of cell surface receptors encoded by the human genome and they play pivotal roles in co-ordinating cellular systems throughout the human body, making them ideal drug targets. Structural biology has played a key role in defining how receptors are activated and signal through G proteins and β-arrestins. The application of structure-based drug design (SBDD) is now yielding novel compounds targeting GPCRs. There is thus significant interest from both academia and the pharmaceutical industry in the structural biology of GPCRs as currently only about one quarter of human non-odorant receptors have had their structure determined. Initially, all the structures were determined by X-ray crystallography, but recent advances in electron cryo-microscopy (cryo-EM) now make GPCRs tractable targets for single-particle cryo-EM with comparable resolution to X-ray crystallography. So far this year, 78% of the 99 GPCR structures deposited in the PDB (Jan–Jul 2021) were determined by cryo-EM. Cryo-EM has also opened up new possibilities in GPCR structural biology, such as determining structures of GPCRs embedded in a lipid nanodisc and multiple GPCR conformations from a single preparation. However, X-ray crystallography still has a number of advantages, particularly in the speed of determining many structures of the same receptor bound to different ligands, an essential prerequisite for effective SBDD. We will discuss the relative merits of cryo-EM and X-ray crystallography for the structure determination of GPCRs and the future potential of both techniques.

Reflections on the Many Facets of Protein Microcrystallography

2014 ◽  
Vol 67 (12) ◽  
pp. 1793 ◽  
Author(s):  
Marion Boudes ◽  
Damià Garriga ◽  
Fasséli Coulibaly
Keyword(s):  
Structural Biology ◽  
State Of The Art ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Structure Based Drug Design ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Many ◽  
The Impact

The use of X-ray crystallography for the structure determination of biological macromolecules has experienced a steady expansion over the last 20 years with the Protein Data Bank growing from <1000 deposited structures in 1992 to >100 000 in 2014. The large number of structures determined each year not only reflects the impact of X-ray crystallography on many disciplines in the biological and medical fields but also its accessibility to non-expert laboratories. Thus protein crystallography is now largely a mainstream research technique and is routinely integrated in high-throughput pipelines such as structural genomics projects and structure-based drug design. Yet, significant frontiers remain that continuously require methodological developments. In particular, membrane proteins, large assemblies, and proteins from scarce natural sources still represent challenging targets for which obtaining the large diffracting crystals required for classical crystallography is often difficult. These limitations have fostered the emergence of microcrystallography, novel approaches in structural biology that collectively aim at determining structures from the smallest crystals. Here, we review the state of the art of macromolecular microcrystallography and recent progress achieved in this field.

From Penicillin to the Ribosome: Revolutions in the Determination and Use of Molecular Structure in Chemistry and Biology

2004 ◽  
Vol 57 (9) ◽  
pp. 829 ◽  
Author(s):  
Edward N. Baker
Keyword(s):  
Biological Sciences ◽  
Molecular Structure ◽  
Structural Genomics ◽  
Structure Determination ◽  
Biological Function ◽  
Structural Information ◽  
Structure Based Drug Design ◽  
X Ray ◽  
X Ray Crystallography

A revolution in structural analysis is in progress in the biological sciences that parallels a similar revolution that took place in chemistry 40–50 years ago. This has major implications for chemistry, offering exciting opportunities at the interface between chemistry and biology. The advances are driven by the value of structural information in biology, for understanding biological function, and for applications in structure-based drug design and structural genomics. Two directions are apparent: towards technically challenging biological structures and assemblies, typified by the potassium channel and the ribosome; and towards high-throughput structure determination of many, smaller, proteins, as in structural genomics. In this review, the advances in molecular biology and in structure determination by X-ray crystallography that make these developments possible are discussed, together with appropriate examples.

scholarly journals From lows to highs: using low-resolution models to phase X-ray data

2013 ◽  
Vol 69 (11) ◽  
pp. 2257-2265 ◽  
Author(s):  
David I. Stuart ◽  
Nicola G. A. Abrescia
Keyword(s):  
Structural Biology ◽  
General Concept ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Phase Extension ◽  
Intact Virus ◽  
Structural Methods

The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ∼13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.

scholarly journals Structure Determination of Membrane Proteins Using X-Ray Crystallography

2021 ◽  
pp. 101-136
Author(s):  
Evan Billings ◽  
Karl Lundquist ◽  
Claire Overly ◽  
Karthik Srinivasan ◽  
Nicholas Noinaj
Keyword(s):  
Membrane Proteins ◽  
Structure Determination ◽  
X Ray ◽  
X Ray Crystallography

The structure determination of a new cembranolide diterpene from the soft coral Lobophytum cristigalli (Coelenterata, Octocorallia, Alcyonacea)

1984 ◽  
Vol 37 (3) ◽  
pp. 545 ◽  
Author(s):  
BF Bowden ◽  
JC Coll ◽  
MSL de Costa ◽  
MF Mackay ◽  
M Mahendran ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Structure Determination ◽  
Soft Coral ◽  
X Ray ◽  
X Ray Crystallography

A specimen of Lobophytum cristigalli collected in Sri Lanka afforded two cembranolide diterpenes (7E,11E,1R,2S,3R,4R,14S)-14-acetoxy-3,4-epoxycembra-7,11,15-trien-17,2-olide (6)* and the corresponding alcohol (7). Their structures were deduced spectroscopically and detailed stereochemistry of (6) was determined by X-ray crystallography.

scholarly journals Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography

2016 ◽  
Vol 2 (2-4) ◽  
pp. 55-68 ◽  
Author(s):  
Zheng Liu ◽  
Tom S. Y. Guu ◽  
Jianhao Cao ◽  
Yinyin Li ◽  
Lingpeng Cheng ◽  
...  
Keyword(s):  
Structure Determination ◽  
Human Virus ◽  
X Ray ◽  
X Ray Crystallography
Sign in / Sign up

Export Citation Format

Share Document