scholarly journals Better together: building protein oligomers naturally and by design

2019 ◽  
Vol 47 (6) ◽  
pp. 1773-1780 ◽  
Author(s):  
Rebecca E.A. Gwyther ◽  
D. Dafydd Jones ◽  
Harley L. Worthy
Keyword(s):  
Function Space ◽  
Structural State ◽  
Protein Structures ◽  
Structure And Function ◽  
New Approach ◽  
Biological Perspective ◽  
Sample Structure ◽  
Single Polypeptide ◽  
Monomeric Proteins ◽  
And Function

Protein oligomers are more common in nature than monomers, with dimers being the most prevalent final structural state observed in known structures. From a biological perspective, this makes sense as it conserves vital molecular resources that may be wasted simply by generating larger single polypeptide units, and allows new features such as cooperativity to emerge. Taking inspiration from nature, protein designers and engineers are now building artificial oligomeric complexes using a variety of approaches to generate new and useful supramolecular protein structures. Oligomerisation is thus offering a new approach to sample structure and function space not accessible through simply tinkering with monomeric proteins.

scholarly journals Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds

2021 ◽  
Vol 8 ◽  
Author(s):  
Nicola Bordin ◽  
Ian Sillitoe ◽  
Jonathan G. Lees ◽  
Christine Orengo
Keyword(s):  
Protein Structure ◽  
Function Space ◽  
Sequence Data ◽  
Protein Structures ◽  
Structure And Function ◽  
Structure Evolution ◽  
Structural Classification ◽  
Protein Sequence Data ◽  
History Of ◽  
And Function

This article is dedicated to the memory of Cyrus Chothia, who was a leading light in the world of protein structure evolution. His elegant analyses of protein families and their mechanisms of structural and functional evolution provided important evolutionary and biological insights and firmly established the value of structural perspectives. He was a mentor and supervisor to many other leading scientists who continued his quest to characterise structure and function space. He was also a generous and supportive colleague to those applying different approaches. In this article we review some of his accomplishments and the history of protein structure classifications, particularly SCOP and CATH. We also highlight some of the evolutionary insights these two classifications have brought. Finally, we discuss how the expansion and integration of protein sequence data into these structural families helps reveal the dark matter of function space and can inform the emergence of novel functions in Metazoa. Since we cover 25 years of structural classification, it has not been feasible to review all structure based evolutionary studies and hence we focus mainly on those undertaken by the SCOP and CATH groups and their collaborators.

New Approach for Researching Forest Ecosystem

2012 ◽  
Vol 472-475 ◽  
pp. 3384-3389
Author(s):  
Zai Qiang Huo ◽  
Xue Qun Zhu
Keyword(s):  
Complex System ◽  
Forest Ecosystem ◽  
Driving Force ◽  
Structure And Function ◽  
The Self ◽  
Self Organization ◽  
New Approach ◽  
Edge Of Chaos ◽  
And Function ◽  
Research Frontiers

It is valuable to be researched in the application of science of complexity to the forest ecosystem. Forest ecosystem is an adaptive complex system which is suggested to be at the edge of chaos or at the criticality. The inner interaction of a forest ecosystem is the main driving force for the self-organization, complexity and order in the forest ecosystem. Forest ecosystem complexity is one of the research frontiers of ecological and evolutionary problems presently. The application of science of complexity to the forest ecosystem complexity studies, its concept, background, methodology and theory are briefly introduced. The forest ecosystem complexity is defined as the structure and function diversity, self-organization and the order of an ecosystem. Its main methods include the cellular automaton, genetic algorithm, game theory, complex network, etc. This paper has discussed mechanism and development of forest ecosystem complexity, by applying the principle and methods of science of complexity, which is a new approach for understanding ecological and evolutionary problems.

scholarly journals A new approach to glycan targeting: enzyme inhibition by oligosaccharide metalloshielding

2014 ◽  
Vol 50 (31) ◽  
pp. 4056-4058 ◽  
Author(s):  
John B. Mangrum ◽  
Brigitte J. Engelmann ◽  
Erica J. Peterson ◽  
John J. Ryan ◽  
Susan J. Berners-Price ◽  
...  
Keyword(s):  
Enzyme Inhibition ◽  
Systematic Study ◽  
Coordination Compounds ◽  
Bioinorganic Chemistry ◽  
Structure And Function ◽  
New Approach ◽  
The Third ◽  
Major Class ◽  
And Function

Metalloglycomics – the effects of defined coordination compounds on oligosaccharides and their structure and function opens new areas for bioinorganic chemistry and expands its systematic study to the third major class of biomolecules after DNA/RNA and proteins.

3. Proteins

2021 ◽  
pp. 34-51
Author(s):  
Mark Lorch
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structure ◽  
Protein Structures ◽  
Structure And Function ◽  
Vast Array ◽  
A Cell ◽  
Cellular Machinery ◽  
And Function ◽  
The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

Membrane proteins: is the future disc shaped?

2016 ◽  
Vol 44 (4) ◽  
pp. 1011-1018 ◽  
Author(s):  
Sarah C. Lee ◽  
Naomi L. Pollock
Keyword(s):  
Membrane Proteins ◽  
Maleic Acid ◽  
Membrane Lipids ◽  
Biological Membranes ◽  
Structure And Function ◽  
Amphiphilic Copolymer ◽  
New Approach ◽  
Analysis Techniques ◽  
Lipid Particles ◽  
And Function

The use of styrene maleic acid lipid particles (SMALPs) for the purification of membrane proteins (MPs) is a rapidly developing technology. The amphiphilic copolymer of styrene and maleic acid (SMA) disrupts biological membranes and can extract membrane proteins in nanodiscs of approximately 10 nm diameter. These discs contain SMA, protein and membrane lipids. There is evidence that MPs in SMALPs retain their native structures and functions, in some cases with enhanced thermal stability. In addition, the method is compatible with biological buffers and a wide variety of biophysical and structural analysis techniques. The use of SMALPs to solubilize and stabilize MPs offers a new approach in our attempts to understand, and influence, the structure and function of MPs and biological membranes. In this review, we critically assess progress with this method, address some of the associated technical challenges, and discuss opportunities for exploiting SMA and SMALPs to expand our understanding of MP biology.

30S ribosomal subunits with fragmented 16S RNA: a new approach for structure and function study of ribosomes

Biochimie ◽  
1991 ◽  
Vol 73 (6) ◽  
pp. 777-787 ◽  
Author(s):  
E. Afonina ◽  
N. Chichkova ◽  
S. Bogdanova ◽  
A. Bogdanov
Keyword(s):  
Structure And Function ◽  
Ribosomal Subunits ◽  
New Approach ◽  
Function Study ◽  
16S Rna ◽  
And Function

PlaneFinder: a methodology to find the best plane for a set of atoms involved in the metal coordination in protein structures

2018 ◽  
Vol 51 (4) ◽  
pp. 1251-1256
Author(s):  
J. Janu Sahana ◽  
S. Sriraghav ◽  
T. A. Vijeth ◽  
T. Nagarushyanth ◽  
R. Santhosh ◽  
...  
Keyword(s):  
Protein Structure ◽  
Efficient Method ◽  
Protein Structures ◽  
Three Dimensional ◽  
Structure And Function ◽  
The Other ◽  
Metal Coordination ◽  
And Function ◽  
Interacting Atoms ◽  
Best Fit

Metal ions play a considerable role in protein structure and function. The roles of most metals and their importance are determined by the arrangements of the interacting atoms in the three-dimensional protein structure. This information is essential in predicting the geometry of the atoms involved in metal coordination. The deviation of the other atoms from the best plane is another crucial factor. The proposed web server, PlaneFinder, provides a fast and efficient method to calculate the best-fit plane for a set of atoms involved in the metal coordination. It provides in addition other possible planes by considering the maximum number of interacting atoms as well as user-selected atoms. The deviations of the selected atoms and other atoms from the best-fit plane are also displayed. PlaneFinder is freely available and can be accessed at http://bioserver1.physics.iisc.ac.in/plane/.

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