Sugarcane Breeding Institute SBI ICAR

Coimbatore, India

Sugarcane Breeding Institute SBI ICAR

Coimbatore, India
SEARCH FILTERS
Time filter
Source Type

Syamaladevi D.P.,National Center for Biological science | Syamaladevi D.P.,Sugarcane Breeding Institute SBI ICAR | Spudich J.A.,National Center for Biological science | Spudich J.A.,Stanford University | Sowdhamini R.,National Center for Biological science
Bioinformatics and Biology Insights | Year: 2011

The myosin superfamily is a versatile group of molecular motors involved in the transport of specific biomolecules, vesicles and organelles in eukaryotic cells. The processivity of myosins along an actin filament and transport of intracellular 'cargo' are achieved by generating physical force from chemical energy of ATP followed by appropriate conformational changes. The typical myosin has a head domain, which harbors an ATP binding site, an actin binding site, and a light-chain bound 'lever arm', followed often by a coiled coil domain and a cargo binding domain. Evolution of myosins started at the point of evolution of eukaryotes, S. cerevisiae being the simplest one known to contain these molecular motors. The coiled coil domain of the myosin classes II, V and VI in whole genomes of several model organisms display differences in the length and the strength of interactions at the coiled coil interface. Myosin II sequences have long-length coiled coil regions that are predicted to have a highly stable dimeric interface. These are interrupted, however, by regions that are predicted to be unstable, indicating possibilities of alternate conformations, associations to make thick filaments, and interactions with other molecules. Myosin V sequences retain intermittent regions of strong and weak interactions, whereas myosin VI sequences are relatively devoid of strong coiled coil motifs. Structural deviations at coiled coil regions could be important for carrying out normal biological function of these proteins. © the author(s), publisher and licensee Libertas Academica Ltd.


Syamaladevi D.P.,National Center for Biological science | Syamaladevi D.P.,Sugarcane Breeding Institute SBI ICAR | Sowdhamini R.,National Center for Biological science
BMC Structural Biology | Year: 2011

Background: Cytoplasmic class XI myosins are the fastest processive motors known. This class functions in high-velocity cytoplasmic streaming in various plant cells from algae to angiosperms. The velocities at which they process are ten times faster than its closest class V homologues. Results: To provide sequence determinants and structural rationale for the molecular mechanism of this fast pace myosin, we have compared the sequences from myosin class V and XI through Evolutionary Trace (ET) analysis. The current study identifies class-specific residues of myosin XI spread over the actin binding site, ATP binding site and light chain binding neck region. Sequences for ET analysis were accumulated from six plant genomes, using literature based text search and sequence searches, followed by triple validation viz. CDD search, string-based searches and phylogenetic clustering. We have identified nine myosin XI genes in sorghum and seven in grape by sequence searches. Both the plants possess one gene product each belonging to myosin type VIII as well. During this process, we have re-defined the gene boundaries for three sorghum myosin XI genes using fgenesh program. Conclusion: Molecular modelling and subsequent analysis of putative interactions involving these class-specific residues suggest a structural basis for the molecular mechanism behind high velocity of plant myosin XI. We propose a model of a more flexible switch I region that contributes to faster ADP release leading to high velocity movement of the algal myosin XI. © 2011 Syamaladevi and Sowdhamini; licensee Bio Med Central Ltd.


Syamaladevi D.P.,National Center for Biological science | Syamaladevi D.P.,Sugarcane Breeding Institute SBI ICAR | Kalaimathy S.,National Center for Biological science | Pasha N.,National Center for Biological science | And 2 more authors.
Proceedings - IEEE International Conference on Data Mining, ICDM | Year: 2011

Profile based sequence search methods are widely used to obtain homologous proteins with the usage of stringent statistical measures. These simple searches, albeit their high sensitivity, cannot solely be relied, while searching for protein families with high functional diversity and sharing structural similarity with other families. Myosins are motor proteins that drive cellular mobility and associated functions in eukaryotes. These motors utilize the chemical energy released by ATP hydrolysis to bring about conformational changes leading to a motor function. The major feature of the protein is a highly conserved head domain which is an ATPase followed by a variable tail that binds to different cargoes. Motor domain is an ATPase that evolved from P-loop containing NTPase ancestral protein. A number of other protein families are believed to be related through divergent evolution of an ancestral P-loop NTP binding motif, hence sequence searches for the members of one superfamily results in cross talks with another. We developed a strategic protocol for effective sequence-based searches of such families. This protocol employs position-specific Iterative Blast followed by a three way validation: 1. Text search scripts 2. clustering using neighbour joining method 3. domain architecture definitions and applied in Myosins from five model genomes as standard. This protocol can be followed for genome scan of similar protein families with sequence wise diverse members and sharing common ancestral structural motifs with other families. © 2011 IEEE.


Syamaladevi D.P.,National Ccentre for Biological science NCBS TIFR | Syamaladevi D.P.,Sugarcane Breeding Institute SBI ICAR | Margaret Sunitha S.,National Ccentre for Biological science NCBS TIFR | Kalaimathy S.,National Ccentre for Biological science NCBS TIFR | And 4 more authors.
Bioinformatics and Biology Insights | Year: 2012

Myosins are one of the largest protein superfamilies with 24 classes. They have conserved structural features and catalytic domains yet show huge variation at different domains resulting in a variety of functions. Myosins are molecules driving various kinds of cellular processes and motility until the level of organisms. These are ATPases that utilize the chemical energy released by ATP hydrolysis to bring about conformational changes leading to a motor function. Myosins are important as they are involved in almost all cellular activities ranging from cell division to transcriptional regulation. They are crucial due to their involvement in many congenital diseases symptomatized by muscular malfunctions, cardiac diseases, deafness, neural and immunological dysfunction, and so on, many of which lead to death at an early age. We present Myosinome, a database of selected myosin classes (myosin II, V, and VI) from five model organisms. This knowledge base provides the sequences, phylogenetic clustering, domain architectures of myosins and molecular models, structural analyses, and relevant literature of their coiled-coil domains. In the current version of Myosinome, information about 71 myosin sequences belonging to three myosin classes (myosin II, V, and VI) in five model organisms (Homo Sapiens, Mus musculus, D. melanogaster, C. elegans and S. cereviseae) identified using bioinformatics surveys are presented, and several of them are yet to be functionally characterized. As these proteins are involved in congenital diseases, such a database would be useful in short-listing candidates for gene therapy and drug development. The database can be accessed from http://caps.ncbs.res.in/myosinome. © the author(s), publisher and licensee Libertas Academica Ltd.


Syamaladevi D.P.,Sugarcane Breeding Institute SBI ICAR | Jayaraman N.,Sugarcane Breeding Institute SBI ICAR | Subramonian N.,Sugarcane Breeding Institute SBI ICAR
Sugar Tech | Year: 2013

Sucrose phosphate phosphatase (SPP) is the last enzyme of sucrose biosynthetic pathway that generates sucrose in an irreversible reaction of sucrose phosphate hydrolysis. Different photosynthetic species have different cytoplasmic sugar levels that can be attributed partly to the variation in specific activity, stability, pH specificity etc. of this key sucrose biosynthesis enzyme which in turn is due to underlying sequence variations. In an attempt to identify the extent of molecular variation we analyzed the evolutionary relationship of domains and conserved segments between its homologues at the amino acid sequence level. In this analysis, we report the differential evolution of the functionally or structurally important conserved regions in SPP. Distance based and character based comparative phylogenetic studies of full length and truncated SPP amino acid sequences revealed the evolutionary relationship between the catalytic S6PP domain and a C-terminal S6PP_C domain of unknown function. The understanding on sequence evolution provides insights to the natural design as well as the modifications that occurred at different regions of SPP during evolution. The current study is the foremost systematic approach to understand the evolutionary features in SPP homologous sequences and in future this study can be extended to unveiling the basis of minute functional variations such as specific activity, stability, pH specificity etc. among the homologues. © 2013 Society for Sugar Research & Promotion.

Loading Sugarcane Breeding Institute SBI ICAR collaborators
Loading Sugarcane Breeding Institute SBI ICAR collaborators