Evolutionary traces decode molecular mechanism behind fast pace of myosin XI

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>viz</it>. 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.</p> <p>Conclusion</p> <p>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.</p

Structural insights on Sucrose transport by Oryza sativa L. Sucrose/H+ Symporter1 (OsSUT1) through refined sequence - template alignment based structural modelling

Sucrose/H+ Symporters (SUTs) play an important role in plant growth and yield. They are involved in long distance transport of sucrose from source leaves to filling grains of cereals through a process called phloem loading. However, the molecular mechanism of sucrose transport through SUTs is not yet known. Understanding the key residues involved in sucrose transport can be helpful in developing high yielding varieties through genetic engineering, gene editing or allele mining. Here, the molecular model of OsSUT1 developed based on refined target-template alignment using Modeller software provides structural insights on the sucrose transport mechanism. We propose 13 putative sucrose binding residues and 11 putative H+ binding residues involved in sucrose/H+ co-transport in OsSUT1

Structural insights on Sucrose transport by Oryza sativa L. Sucrose/H+ Symporter1 (OsSUT1) through refined sequence - template alignment based structural modelling

283-290Sucrose/H+ Symporters (SUTs) play an important role in plant growth and yield. They are involved in long distance transport of sucrose from source leaves to filling grains of cereals through a process called phloem loading. However, the molecular mechanism of sucrose transport through SUTs is not yet known. Understanding the key residues involved in sucrose transport can be helpful in developing high yielding varieties through genetic engineering, gene editing or allele mining. Here, the molecular model of OsSUT1 developed based on refined target-template alignment using Modeller software provides structural insights on the sucrose transport mechanism. We propose 13 putative sucrose binding residues and 11 putative H+ binding residues involved in sucrose/H+ co-transport in OsSUT1

Structural and Functional Insights on the Myosin Superfamily

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Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships

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