Structural Analysis of Proteins on Lipid Substrates

2000 ◽  
Vol 6 (S2) ◽  
pp. 1182-1183
Author(s):  
Elizabeth M. Wilson-Kubalek
Keyword(s):  
Structural Information ◽  
Rapid Determination ◽  
3D Structure ◽  
Three Dimensional ◽  
Molecular Complexes ◽  
Structural Data ◽  
X Ray Crystallography ◽  
Helical Protein ◽  
3D Structure Determination

Electron microscopy (EM) has become an increasingly powerful method for the determination of three-dimensional (3D) structures of proteins and macromolecular complexes. EM offers advantages over X-ray crystallography and NMR for obtaining structural information about proteins in physiological conditions, as components of large assemblies, that cannot be obtained in large quantity, or that fail to yield 3D crystals. EM has been used to obtain structural data from images of isolated molecules and molecular complexes, two-dimensional (2D) protein crystals, and helical protein arrays. Helically arranged proteins allow the most rapid determination of 3D maps because they contain a complete range of equally spaced molecular views, therefore no tilting of the sample with respect to the electron beam is required. However, so far 3D structure determination of helical assemblies has been limited to proteins that naturally adopt this organization and to proteins that fortuitously crystallize as helices.

scholarly journals Ribosolve: Rapid determination of three-dimensional RNA-only structures

2019 ◽  
Author(s):  
Kalli Kappel ◽  
Kaiming Zhang ◽  
Zhaoming Su ◽  
Wipapat Kladwang ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Rapid Determination ◽  
3D Structure ◽  
Three Dimensional ◽  
Internal Controls ◽  
Full Length ◽  
Chemical Mapping ◽  
Rna Molecules ◽  
Moderate Resolution ◽  
3D Structure Determination

AbstractThe discovery and design of biologically important RNA molecules is dramatically outpacing three-dimensional structural characterization. To address this challenge, we present Ribosolve, a hybrid method integrating moderate-resolution cryo-EM maps, chemical mapping, and Rosetta computational modeling, and demonstrate its application to thirteen previously unknown 119-to 338-nucleotide protein-free RNA-only structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length V. cholerae and F. nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and computer-designed spinach-TTR-3, eterna3D-JR_1, and ATP-TTR-3 with and without AMP. Blind challenges, prospective compensatory mutagenesis, internal controls, and simulation benchmarks validate the Ribosolve models and establish that modeling convergence is quantitatively predictive of model accuracy. These results demonstrate that RNA-only 3D structure determination can be rapid and routine.

scholarly journals The young person’s guide to the PDB

2016 ◽  
Vol 62 (3) ◽  
pp. 242-249
Author(s):  
Wladek Minor ◽  
Zbigniew Dauter ◽  
Mariusz Jaskolski
Keyword(s):  
Structural Information ◽  
Three Dimensional ◽  
Data Bank ◽  
Research Process ◽  
Protein Crystal ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Three Dimensional Models ◽  
Training Skill

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120,000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.

scholarly journals 3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy

2016 ◽  
Vol 52 (67) ◽  
pp. 10237-10240 ◽  
Author(s):  
Bin-Bin Pan ◽  
Feng Yang ◽  
Yansheng Ye ◽  
Qiong Wu ◽  
Conggang Li ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Structure Determination ◽  
3D Structure ◽  
Three Dimensional ◽  
Living Cells ◽  
Paramagnetic Nmr ◽  
Dimensional Structure ◽  
Site Specific ◽  
3D Structure Determination

The integration of site-specific labeling of proteins with a stable lanthanide binding tag, paramagnetic NMR spectroscopy and the GPS-Rosetta program presents an effective and fast way of determining the three-dimensional structure of a protein in living cells.

Rapid determination of fractal structure of bacterial assemblages in wastewater treatment: implications to process optimisation

1998 ◽  
Vol 38 (2) ◽  
pp. 9-15 ◽  
Author(s):  
J. Guan ◽  
T. D. Waite ◽  
R. Amal ◽  
H. Bustamante ◽  
R. Wukasch
Keyword(s):  
Wastewater Treatment ◽  
Fractal Structure ◽  
Structural Information ◽  
Rapid Determination ◽  
Fractal Dimensions ◽  
Structure Information ◽  
Treatment Processes ◽  
On Line ◽  
Bacterial Aggregates

A rapid method of determining the structure of aggregated particles using small angle laser light scattering is applied here to assemblages of bacteria from wastewater treatment systems. The structure information so obtained is suggestive of fractal behaviour as found by other methods. Strong dependencies are shown to exist between the fractal structure of the bacterial aggregates and the behaviour of the biosolids in zone settling and dewatering by both pressure filtration and centrifugation methods. More rapid settling and significantly higher solids contents are achievable for “looser” flocs characterised by lower fractal dimensions. The rapidity of determination of structural information and the strong dependencies of the effectiveness of a number of wastewater treatment processes on aggregate structure suggests that this method may be particularly useful as an on-line control tool.

scholarly journals 3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography

2012 ◽  
Vol 180 (2) ◽  
pp. 318-326 ◽  
Author(s):  
Ke Wang ◽  
Korrinn Strunk ◽  
Gongpu Zhao ◽  
Jennifer L. Gray ◽  
Peijun Zhang
Keyword(s):  
Structure Determination ◽  
Mammalian Cells ◽  
Electron Tomography ◽  
3D Structure ◽  
Cryo Electron Tomography ◽  
3D Structure Determination

A current assessment of photosystem II structure

1996 ◽  
Vol 16 (2) ◽  
pp. 159-187 ◽  
Author(s):  
William V. Nicholson ◽  
Robert C. Ford ◽  
Andreas Holzenburg
Keyword(s):  
Photosystem Ii ◽  
Structural Information ◽  
Three Dimensional ◽  
Structural Data ◽  
X Ray Diffraction ◽  
Membrane Protein Complex ◽  
Fast Absorption ◽  
Current Assessment ◽  
Electron Microscopical ◽  
A Current

This review covers the recent progress in the elucidation of the structure of photosystem II (PSII). Because much of the structural information for this membrane protein complex has been revealed by electron microscopy (EM), the review will also consider the specific technical and interpretation problems that arise with EM where they are of particular relevance to the structural data. Most recent reviews of photosystem II structure have concentrated on molecular studies of the PSII genes and on the likely roles of the subunits that they encode or they were mainly concerned with the biophysical data and fast absorption spectroscopy largely relating to electron transfer in various purified PSII preparations. In this review, we will focus on the approaches to the three-dimensional architecture of the complex and the lipid bilayer in which it is located (the thylakoid membrane) with special emphasis placed upon electron microscopical studies of PSII-containing thylakoid membranes. There are a few reports of 3D crystals of PSII and of associated X-ray diffraction measurements and although little structural information has so far been obtained from such studies (because of the lack of 3D crystals of sufficient quality), the prospects for such studies are also assessed.

scholarly journals 3D structure determination of amyloid fibrils using solid-state NMR spectroscopy

Methods ◽  
2018 ◽  
Vol 138-139 ◽  
pp. 26-38 ◽  
Author(s):  
Antoine Loquet ◽  
Nadia El Mammeri ◽  
Jan Stanek ◽  
Mélanie Berbon ◽  
Benjamin Bardiaux ◽  
...  
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Solid State Nmr ◽  
Amyloid Fibrils ◽  
3D Structure ◽  
Solid State Nmr Spectroscopy ◽  
3D Structure Determination

scholarly journals Protein Structure Determination in Living Cells

2019 ◽  
Vol 20 (10) ◽  
pp. 2442 ◽  
Author(s):  
Teppei Ikeya ◽  
Peter Güntert ◽  
Yutaka Ito
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Structural Information ◽  
Nuclear Overhauser Effect ◽  
Protein Structures ◽  
Three Dimensional ◽  
Structural Data ◽  
Sample Tube ◽  
In Cells

To date, in-cell NMR has elucidated various aspects of protein behaviour by associating structures in physiological conditions. Meanwhile, current studies of this method mostly have deduced protein states in cells exclusively based on ‘indirect’ structural information from peak patterns and chemical shift changes but not ‘direct’ data explicitly including interatomic distances and angles. To fully understand the functions and physical properties of proteins inside cells, it is indispensable to obtain explicit structural data or determine three-dimensional (3D) structures of proteins in cells. Whilst the short lifetime of cells in a sample tube, low sample concentrations, and massive background signals make it difficult to observe NMR signals from proteins inside cells, several methodological advances help to overcome the problems. Paramagnetic effects have an outstanding potential for in-cell structural analysis. The combination of a limited amount of experimental in-cell data with software for ab initio protein structure prediction opens an avenue to visualise 3D protein structures inside cells. Conventional nuclear Overhauser effect spectroscopy (NOESY)-based structure determination is advantageous to elucidate the conformations of side-chain atoms of proteins as well as global structures. In this article, we review current progress for the structure analysis of proteins in living systems and discuss the feasibility of its future works.

scholarly journals SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

2020 ◽  
Vol 36 (11) ◽  
pp. 3372-3378
Author(s):  
Alexander Gress ◽  
Olga V Kalinina
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Structural Data ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Precise Measure ◽  
The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

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.

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