scholarly journals Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules

2016 ◽  
Vol 25 (3) ◽  
pp. 754-768 ◽  
Author(s):  
Rei Matsuoka ◽  
Atsushi Shimada ◽  
Yasuaki Komuro ◽  
Yuji Sugita ◽  
Daisuke Kohda
Keyword(s):  
Spatial Distribution ◽  
Free Space ◽  
Rational Design ◽  
Protein Crystals ◽  
Protein Molecules ◽  
Contact Free ◽  
Crystal Contact

scholarly journals Intentional crystal-contact-free space in protein crystal

2014 ◽  
Vol 70 (a1) ◽  
pp. C339-C339
Author(s):  
Rei Matsuoka ◽  
Yasuaki Komuro ◽  
Yuji Sugita ◽  
Daisuke Kohda
Keyword(s):  
Electron Density ◽  
Free Space ◽  
Protein Import ◽  
Model Building ◽  
Protein Complexes ◽  
Dynamics Simulation ◽  
Protein Crystal ◽  
Α Helix ◽  
Contact Free ◽  
Crystal Contact

To understand the function of proteins, it is essential to perform the structural analysis of the protein complexes with ligands, such as substrates or partner molecules. The motions of ligands are restricted by the contacts with neighbor protein molecules in the crystal lattice. Here, we propose a new technique to analyze dynamics of a ligand in the bound state preserved in the crystal-contact-free space, which is intentionally created in protein crystals. We used Tom20 as a target protein. Tom20 functions as a general protein import receptor, by recognizing N-terminal signal sequences (presequences) of mitochondrial matrix proteins. Our working hypothesis is that the promiscuous specificity of Tom20 is attributed to the large mobility of the presequneces in the binding groove of Tom20 (1,2). Our aim is to obtain electron density that reflects the large mobility of a presequence in the crystal-contact-free space. In order to create the crystal-contact-free space, we took advantage of a protein fused with maltose binding protein (MBP). The key of the design is the connection of the two proteins firmly. We fused the C-terminal α-helix of MBP and the N-terminal α-helix of Tom20 seamlessly. After a systematic model building study, we decided to use a design with four residues inserted in the linker region. We found smeared electron density in the binding site of presequences in the difference Fourier electron-density map. We attached an iodine atom at the N-terminus of the presequence and confirmed the N-terminal position in the smeared electron density. We performed molecular dynamics simulation without the tethering in solution (3). The electron density simulated from the MD trajectory was fully consistent with the smeared electron density in the crystal contact-free space. We concluded that the smeared electron density corresponded to the partially overlapping region of the multiple states of the bound presequence.

scholarly journals Multi-material 3D printed mechanical metamaterials: Rational design of elastic properties through spatial distribution of hard and soft phases

2018 ◽  
Vol 113 (24) ◽  
pp. 241903 ◽  
Author(s):  
M. J. Mirzaali ◽  
A. Caracciolo ◽  
H. Pahlavani ◽  
S. Janbaz ◽  
L. Vergani ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Elastic Properties ◽  
Rational Design ◽  
Mechanical Metamaterials ◽  
3D Printed

scholarly journals Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study

2020 ◽  
Vol 1864 (2) ◽  
pp. 129418 ◽  
Author(s):  
Siqin Bala ◽  
Shoko Shinya ◽  
Arpita Srivastava ◽  
Marie Ishikawa ◽  
Atsushi Shimada ◽  
...  
Keyword(s):  
Protein Crystal ◽  
Flexible Loop ◽  
Contact Free ◽  
Crystal Contact

The Scope, Functions, and Dynamics of Posttranslational Protein Modifications

2019 ◽  
Vol 70 (1) ◽  
pp. 119-151 ◽  
Author(s):  
A. Harvey Millar ◽  
Joshua L. Heazlewood ◽  
Carmela Giglione ◽  
Michael J. Holdsworth ◽  
Andreas Bachmair ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Posttranslational Modification ◽  
Subcellular Distribution ◽  
Protein Function ◽  
Protein Molecule ◽  
Plant Biology ◽  
Protein Molecules ◽  
N Terminus ◽  
Functional Implications ◽  
Combined Action

Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.

scholarly journals Penetration of dyes into protein crystals

2019 ◽  
Vol 75 (2) ◽  
pp. 132-140 ◽  
Author(s):  
Alexander McPherson
Keyword(s):  
Molecular Weight ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Dye Molecules ◽  
Molecular Weight Range ◽  
Interacting Protein ◽  
Dye Penetration ◽  
Pure Diffusion ◽  
Protein Molecules ◽  
Degree Of Association

Experiments were carried out on 15 different protein crystals with the objective of estimating the rates of penetration of dye molecules into the crystals. The dyes were in the molecular-weight range 250–1000 Da and the protein crystals were of dimensions of 0.7 mm or greater. Experiments were also conducted on protein crystals grown between glass cover slips (separation 200 µm) that restricted the direction of diffusion. The rate of penetration of dyes into protein crystals depends very much on the degree of association between the dye and protein molecules. Dye penetration was not consistent with pure diffusion when the affinity of the protein for the dye was significant, and this was frequent. Penetration rates were less dependent on factors such as the molecular weight of the dye or the diffusion direction. For weakly interacting protein crystal/dye combinations, penetration was a fair measure of diffusivity and the observed rates were in the range 60–100 µm h−1. For strongly interacting combinations, the rates of penetration were of the order of 15–30 µm h−1.

scholarly journals Analyses for spatial distribution of buried hydrophobic sidechains in protein molecules

2003 ◽  
Vol 43 (supplement) ◽  
pp. S213
Author(s):  
T. Tanaka ◽  
Y. Kuroda ◽  
S. Yokoyama
Keyword(s):  
Spatial Distribution ◽  
Protein Molecules

Spatial distribution of protein molecules adsorbed at a polyelectrolyte multilayer

2005 ◽  
Vol 71 (4) ◽  
Author(s):  
Guido Jackler ◽  
Claus Czeslik ◽  
Roland Steitz ◽  
Catherine A. Royer
Keyword(s):  
Spatial Distribution ◽  
Polyelectrolyte Multilayer ◽  
Protein Molecules
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