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/.

mirror, a Drosophila homeobox gene in the Iroquois complex, is required for sensory organ and alula formation

Development ◽  
1998 ◽  
Vol 125 (7) ◽  
pp. 1217-1227 ◽  
Author(s):  
B.T. Kehl ◽  
K.O. Cho ◽  
K.W. Choi
Keyword(s):  
Protein Structure ◽  
Genetic Analysis ◽  
Genetic Map ◽  
Body Wall ◽  
Homeobox Gene ◽  
Structure And Function ◽  
The Other ◽  
Complex Region ◽  
Sensory Bristles ◽  
And Function

The Drosophila notum, the dorsal body wall of the thorax, is subdivided genetically into longitudinal domains (Calleja, M., Moreno, E., Pelaz, S. and Morata, G. (1996) Science 274, 252–255). Two homeobox genes clustered in the iroquois complex, araucan and caupolican, regulate proneural genes and are required for development of sensory bristles in the lateral notum (Gomez-Skarmeta, J. L., del Corral, R. D., de la Calle-Mustienes, E., Ferres-Marco, D. and Modolell, J. (1996) Cell 85, 95–105). An iroquois-related homeobox gene, mirror, was recently isolated and is localized close to the iroquois complex region (McNeil, H., Yang, C.-H., Brodsky, M., Ungos, J. and Simon, M. A. (1997) Genes and Development 11, 1073–1082; this study). We show that mirror is required for the formation of the alula and a subset of sensory bristles in the lateral domain of the notum. Genetic analysis suggests that mirror and the other iroquois genes interact to form the alula as well as the sensory organs. Based on similarities between mirror and the iroquois genes in their genetic map positions, expression, protein structure and function, mirror is considered a new member of the iroquois complex and is involved in prepatterning sensory precursor cells in the lateral notum.

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.

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.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

Order-disorder transitions of cytoplasmic N-termini in the mechanisms of P-type ATPases

2020 ◽  
Author(s):  
Khondker Rufaka Hossain ◽  
Daniel Clayton ◽  
Sophia C Goodchild ◽  
Alison Rodger ◽  
Richard James Payne ◽  
...  
Keyword(s):  
Protein Structure ◽  
Membrane Protein ◽  
Structure And Function ◽  
Membrane Protein Structure ◽  
Protein Structure And Function ◽  
Lipid Environment ◽  
Membrane Pumps ◽  
And Function ◽  
P Type

Membrane protein structure and function are modulated via interactions with their lipid environment. This is particularly true for the integral membrane pumps, the P-type ATPases. These ATPases play vital roles...

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