scholarly journals Structural Systems Biology and Multiscale Signaling Models

2012 ◽  
Vol 40 (11) ◽  
pp. 2295-2306 ◽  
Author(s):  
Shannon E. Telesco ◽  
Ravi Radhakrishnan
Keyword(s):  
Systems Biology ◽  
Structural Systems ◽  
Structural Systems Biology

Small-angle X-ray and neutron scattering as a tool for structural systems biology

2010 ◽  
Vol 391 (7) ◽  
Author(s):  
Dmitri I. Svergun
Keyword(s):  
Systems Biology ◽  
Neutron Scattering ◽  
Conformational Changes ◽  
Small Angle ◽  
Structural Systems ◽  
Biological Macromolecules ◽  
X Rays ◽  
Hierarchical Systems ◽  
X Ray ◽  
Structural Systems Biology

Abstract Small-angle scattering (SAS) of X-rays and neutrons reveals low-resolution structures of biological macromolecules in solution. With the recent experimental and methodological advances, SAS became a unique tool for characterising biological systems. The method covers an extremely broad range of molecule sizes (from a few kDa to hundreds of MDa) and experimental conditions (temperature, pH, salinity, ligand addition, etc.), which is of primary importance for a systemic approach in structural biology. The method provides unique information about the overall structure and conformational changes of native individual proteins, functional complexes, flexible macromolecules and hierarchical systems. New developments in small-angle X-ray and neutron scattering studies of biological macromolecules in solution are briefly reviewed, with a special emphasis on technical and methodological approaches useful for structural systems biology. Possibilities of synergistic use of the method with other techniques are considered.

scholarly journals Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

Science ◽  
2013 ◽  
Vol 340 (6137) ◽  
pp. 1220-1223 ◽  
Author(s):  
Roger L. Chang ◽  
Kathleen Andrews ◽  
Donghyuk Kim ◽  
Zhanwen Li ◽  
Adam Godzik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Systems Biology ◽  
Structural Information ◽  
Protein Structures ◽  
Limiting Factors ◽  
Scale Model ◽  
Structural Systems ◽  
A Genome ◽  
Structural Systems Biology ◽  
Genome Scale

Genome-scale network reconstruction has enabled predictive modeling of metabolism for many systems. Traditionally, protein structural information has not been represented in such reconstructions. Expansion of a genome-scale model of Escherichia coli metabolism by including experimental and predicted protein structures enabled the analysis of protein thermostability in a network context. This analysis allowed the prediction of protein activities that limit network function at superoptimal temperatures and mechanistic interpretations of mutations found in strains adapted to heat. Predicted growth-limiting factors for thermotolerance were validated through nutrient supplementation experiments and defined metabolic sensitivities to heat stress, providing evidence that metabolic enzyme thermostability is rate-limiting at superoptimal temperatures. Inclusion of structural information expanded the content and predictive capability of genome-scale metabolic networks that enable structural systems biology of metabolism.

scholarly journals cellPACK: a virtual mesoscope to model and visualize structural systems biology

2014 ◽  
Vol 12 (1) ◽  
pp. 85-91 ◽  
Author(s):  
Graham T Johnson ◽  
Ludovic Autin ◽  
Mostafa Al-Alusi ◽  
David S Goodsell ◽  
Michel F Sanner ◽  
...  
Keyword(s):  
Systems Biology ◽  
Structural Systems ◽  
Structural Systems Biology

Structural Systems Biology: Modeling Interactions and Networks for Systems Studies

2014 ◽  
pp. 9-19
Author(s):  
Robert B. Russell, ◽  
Gordana Apic ◽  
Olga Kalinina ◽  
Leonardo Trabuco ◽  
Matthew J. Betts ◽  
...  
Keyword(s):  
Systems Biology ◽  
Structural Systems ◽  
Modeling Interactions ◽  
Structural Systems Biology ◽  
Systems Studies

scholarly journals A Structural Systems Biology Approach for Quantifying the Systemic Consequences of Missense Mutations in Proteins

2012 ◽  
Vol 8 (10) ◽  
pp. e1002738 ◽  
Author(s):  
Tammy M. K. Cheng ◽  
Lucas Goehring ◽  
Linda Jeffery ◽  
Yu-En Lu ◽  
Jacqueline Hayles ◽  
...  
Keyword(s):  
Systems Biology ◽  
Structural Systems ◽  
Missense Mutations ◽  
Structural Systems Biology

scholarly journals Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach

2008 ◽  
Vol 2 (1) ◽  
Author(s):  
Najl V Valeyev ◽  
Declan G Bates ◽  
Pat Heslop-Harrison ◽  
Ian Postlethwaite ◽  
Nikolay V Kotov
Keyword(s):  
Systems Biology ◽  
Structural Systems ◽  
Structural Systems Biology
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