scholarly journals Atomic-level accuracy in simulations of large protein crystals.

1994 ◽  
Vol 91 (18) ◽  
pp. 8715-8718 ◽  
Author(s):  
D. M. York ◽  
A. Wlodawer ◽  
L. G. Pedersen ◽  
T. A. Darden
2008 ◽  
Vol 64 (a1) ◽  
pp. C247-C248
Author(s):  
N. Shimizu ◽  
H. Yoshikawa ◽  
M. Adachi ◽  
T. Tamada ◽  
K. Hidaka ◽  
...  

2010 ◽  
Vol 43 (4) ◽  
pp. 937-939 ◽  
Author(s):  
Keisuke Kakinouchi ◽  
Tsutomu Nakamura ◽  
Taro Tamada ◽  
Hiroaki Adachi ◽  
Shigeru Sugiyama ◽  
...  

A method for growing large protein crystals is described. In this method, a cut pipette tip is used to hang large-scale droplets (maximum volume 200 µl) consisting of protein and precipitating agents. A crystal grows at the vapor–liquid interface; thereafter the grown crystal can be retrieved by droplet–droplet contact both for repeated macroseeding and for mounting crystals in a capillary. Crystallization experiments with peroxiredoxin ofAeropyrum pernixK1 (thioredoxin peroxidase, ApTPx) and hen egg white lysozyme demonstrated that this large-scale hanging-drop method could produce a large-volume crystal very effectively. A neutron diffraction experiment confirmed that an ApTPx crystal (6.2 mm3) obtained by this method diffracted to beyond 3.5 Å resolution.


2001 ◽  
Vol 34 (3) ◽  
pp. 388-391 ◽  
Author(s):  
Genpei Li ◽  
Ye Xiang ◽  
Ying Zhang ◽  
Da-Cheng Wang

The rate of water vaporization in the vapor-diffusion method is critical for the protein crystallization process. Present methods, however, allow little or no control of the equilibration rates. This paper presents a relatively simple innovation of the conventional vapor-diffusion method by introducing a capillary barrier (for hanging drop) or a punched film barrier (for both hanging and sitting drop) between drop and reservoir, which can be beneficial in controlling the water vaporization rate, thereby promoting growth of large protein crystals. The crystallization experiments for lysozyme, trichosanthin and a novel neurotoxin BmK Mu9 show that this modified vapor-controlling-diffusion method is very effective for producing large protein crystals. The improved technique can be routinely used as a method for the preparation of other macromolecular and small-molecule crystals whose crystallization involves vaporization of water.


2016 ◽  
Vol 452 ◽  
pp. 172-178 ◽  
Author(s):  
Mihoko Maruyama ◽  
Yuki Hayashi ◽  
Hiroshi Y. Yoshikawa ◽  
Shino Okada ◽  
Haruhiko Koizumi ◽  
...  

2010 ◽  
Vol 18 (1) ◽  
pp. 16-19 ◽  
Author(s):  
Hiroyoshi Matsumura ◽  
Shigeru Sugiyama ◽  
Mika Hirose ◽  
Keisuke Kakinouchi ◽  
Mihoko Maruyama ◽  
...  

2020 ◽  
Vol 76 (12) ◽  
pp. 1174-1183
Author(s):  
Hirohiko Nakamura ◽  
Sachiko Takahashi ◽  
Koji Inaka ◽  
Hiroaki Tanaka

A large high-quality crystal is required to specify the positions of H atoms in neutron structural analysis. Consequently, several methods have been proposed for obtaining such large crystals, and theoretical considerations for growing them have been presented. However, further investigation is required to obtain a numerical model that can provide quantitative experimental conditions for obtaining a single large crystal. In the case of protein crystallization experiments, the amount of sample is often limited. Therefore, it is more realistic to make a rough estimation from a small number of experiments. This paper proposes a method of estimating the optimum experimental conditions for the growth of large protein crystals by performing a small number of experiments using a micro-batch method and reporting a numerical model based on nucleation theory and a linear approximation of the crystal-growth rate. Specifically, micro-batch experiments are performed to provide the empirical parameters for the model and to help to estimate the conditions for the growth of a crystal of a predetermined size using a certain sample concentration and volume. This method is offered as a step on the path towards efficiently and rationally producing large crystals that can be subjected to neutron diffraction without depending on luck or on performing many experiments. It is expected to contribute to drug design and the elucidation of protein molecular functions and mechanisms by obtaining positional information on H atoms in the protein molecule, which is an advantage of neutron diffraction.


2019 ◽  
Vol 75 (a1) ◽  
pp. a426-a426
Author(s):  
Koji Inaka ◽  
Sachiko Takahashi ◽  
Bin Yan ◽  
Misako Koga ◽  
Yoshinobu Hashizume ◽  
...  

2018 ◽  
Vol 74 (a1) ◽  
pp. a330-a330
Author(s):  
Hiroaki Tanaka ◽  
Sachiko Takahashi ◽  
Bin Yan ◽  
Misako Koga ◽  
Masayuki Kamo ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document