scholarly journals Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

2012 ◽  
Vol 14 (6) ◽  
pp. 724-736 ◽  
Author(s):  
M. Maadooliat ◽  
X. Gao ◽  
J. Z. Huang
Keyword(s):  
Sampling Methods ◽  
Conformational Sampling

Simple, yet powerful methodologies for conformational sampling of proteins

2015 ◽  
Vol 17 (9) ◽  
pp. 6155-6173 ◽  
Author(s):  
Ryuhei Harada ◽  
Yu Takano ◽  
Takeshi Baba ◽  
Yasuteru Shigeta
Keyword(s):  
Protein Folding ◽  
Large Amplitude ◽  
Sampling Methods ◽  
Substrate Binding ◽  
Conformational Sampling ◽  
T4 Lysozyme ◽  
Induced Fit ◽  
Feature Article ◽  
Loop Region ◽  
Small Proteins

This feature article reviews four different conformational sampling methods for proteins recently developed by us. We here deal with protein folding of small proteins, large amplitude domain motion of T4 lysozyme, and induced-fit motion of a loop region after substrate binding using our methods.

Going Beyond 3-D Imaging: Automated 3-D Montaged image Analysis of Cytological Specimens

1996 ◽  
Vol 54 ◽  
pp. 282-283
Author(s):  
Badrinath Roysam ◽  
Hakan Ancin ◽  
Douglas E. Becker ◽  
Robert W. Mackin ◽  
Matthew M. Chestnut ◽  
...  
Keyword(s):  
Image Analysis ◽  
Structural Changes ◽  
Sampling Methods ◽  
Spatial Clustering ◽  
Three Dimensional ◽  
Field Of View ◽  
Cell Counting ◽  
Depth Of Field ◽  
Tissue Cell ◽  
Tissue Organization

This paper summarizes recent advances made by this group in the automated three-dimensional (3-D) image analysis of cytological specimens that are much thicker than the depth of field, and much wider than the field of view of the microscope. The imaging of thick samples is motivated by the need to sample large volumes of tissue rapidly, make more accurate measurements than possible with 2-D sampling, and also to perform analysis in a manner that preserves the relative locations and 3-D structures of the cells. The motivation to study specimens much wider than the field of view arises when measurements and insights at the tissue, rather than the cell level are needed.The term “analysis” indicates a activities ranging from cell counting, neuron tracing, cell morphometry, measurement of tracers, through characterization of large populations of cells with regard to higher-level tissue organization by detecting patterns such as 3-D spatial clustering, the presence of subpopulations, and their relationships to each other. Of even more interest are changes in these parameters as a function of development, and as a reaction to external stimuli. There is a widespread need to measure structural changes in tissue caused by toxins, physiologic states, biochemicals, aging, development, and electrochemical or physical stimuli. These agents could affect the number of cells per unit volume of tissue, cell volume and shape, and cause structural changes in individual cells, inter-connections, or subtle changes in higher-level tissue architecture. It is important to process large intact volumes of tissue to achieve adequate sampling and sensitivity to subtle changes. It is desirable to perform such studies rapidly, with utmost automation, and at minimal cost. Automated 3-D image analysis methods offer unique advantages and opportunities, without making simplifying assumptions of tissue uniformity, unlike random sampling methods such as stereology.12 Although stereological methods are known to be statistically unbiased, they may not be statistically efficient. Another disadvantage of sampling methods is the lack of full visual confirmation - an attractive feature of image analysis based methods.

Flavin radicals, conformational sampling and robust design principles in interprotein electron transfer: the trimethylamine dehydrogenase-electron-transferring flavoprotein complex

2004 ◽  
Vol 71 ◽  
pp. 1-14
Author(s):  
David Leys ◽  
Jaswir Basran ◽  
François Talfournier ◽  
Kamaldeep K. Chohan ◽  
Andrew W. Munro ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Kinetic Studies ◽  
Molecular Assembly ◽  
Conformational Sampling ◽  
Trimethylamine Dehydrogenase ◽  
Key Residues ◽  
Electron Transferring Flavoprotein ◽  
Electron Transfer Complex

TMADH (trimethylamine dehydrogenase) is a complex iron-sulphur flavoprotein that forms a soluble electron-transfer complex with ETF (electron-transferring flavoprotein). The mechanism of electron transfer between TMADH and ETF has been studied using stopped-flow kinetic and mutagenesis methods, and more recently by X-ray crystallography. Potentiometric methods have also been used to identify key residues involved in the stabilization of the flavin radical semiquinone species in ETF. These studies have demonstrated a key role for 'conformational sampling' in the electron-transfer complex, facilitated by two-site contact of ETF with TMADH. Exploration of three-dimensional space in the complex allows the FAD of ETF to find conformations compatible with enhanced electronic coupling with the 4Fe-4S centre of TMADH. This mechanism of electron transfer provides for a more robust and accessible design principle for interprotein electron transfer compared with simpler models that invoke the collision of redox partners followed by electron transfer. The structure of the TMADH-ETF complex confirms the role of key residues in electron transfer and molecular assembly, originally suggested from detailed kinetic studies in wild-type and mutant complexes, and from molecular modelling.

Pengaruh Tekanan Waktu, Locus Of Control , Tindakan Supervisi, Dan Materialitas Terhadap Penghentian Prematur Atas Prosedur Audit Studi Kasus Pada Kantor Akuntan Publik Daerah Istimewa Yogyakarta Tahun 2015

2017 ◽  
Vol 24 (1) ◽  
pp. 35-53
Author(s):  
Sulastiningsih Sulastiningsih ◽  
Intan Ayu Candra
Keyword(s):  
Locus Of Control ◽  
Premature Termination ◽  
Sampling Methods ◽  
Time Pressure ◽  
Linear Regression Analysis ◽  
Multiple Linear Regression Analysis ◽  
Test Reliability ◽  
Friedman Test ◽  
Independent Variables ◽  
Public Accountant

The purpose of this study is to prove: (1) Time pressure, locus of control, the action of supervision and materiality partially affect the premature termination of the audit procedures (2) Time pressure, locus of control, supervision and materiality simultaneously affect the premature termination on the audit procedures. This research was conducted in Public Accountant firm in Yogyakarta region of which total 12 samples of KAP, by distributing 105 questionnaires, and 57 questionnaires were returned (54%). 34 of the returned questionnaires can be processed (34%). The samples in this study were determined by using non-probability sampling, one of purposive sampling methods. Data analysis consisted of: (1) validity test, reliability test and classical assumption. The result showed that the instruments used are quite reliable and valid (2) multiple linear regression analysis. The results are (a) Some of independent variables partially affect premature termination of the audit procedure, while the action of supervision does not influence premature termination of audit procedures (b) All independent variables influence simultaneously to the premature termination of the audit procedures (c) All independent variables showed that as much as 55% it affects on premature termination of the audit procedures, the rest of it are influenced by other variables. (3) Friedman Test. The result shows that there are order of priority of audit procedures being terminated.

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