Role Of Cellular Environment Research Articles

Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu

Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder-concentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.

A calcium dependent protein kinase involves H2O2 mediated guard cell signaling in Aarabidopsis

Drought is a major threat for plant growth and productivity. Plants lose over 90% of water by transpiration through stomatal pores. The cytosolic free Ca2+ elevated in guard cells in response to stress stimuli triggers stomatal closure. The plant-specific calcium-dependent protein kinases (CDPKs) play important roles in regulating downstream components of calcium signaling. In this study the biological function of Arabidopsis calcium dependent protein kinase, CPK8, in response to ABA signaling in guard cells was characterized. The plants of TDNA insertion mutant of cpk8 were more sensitive to drought stress than wild-type plants. The GUS staining studies confirmed that CPK8 expressed in leaves, specifically in guard cells. RT-PCR analysis showed that CPK8 expression was induced in response to drought stress. Further, pre-opened cpk8 stomata failed to close in response to H2O2 and Ca2+, which is consistent with the inability of cpk8 plants to reduce water loss upon drought. The drought susceptibility and stomatal impairment in response to H2O2 and Ca2+ of the cpk8 implicated that CPK8 plays a role in cellular environment in the control of H2O2 homeostasis and also as a compulsory molecule in the transduction of H2O2 signal in guard cells in response to drought stress. Tropical Agricultural Research and Extension 16(1): 2013: page 7-14

Computational prediction of SEG (single exon gene) function in humans

Human genes are often interrupted by non-coding, intragenic sequences called introns. Hence, the gene sequence is divided into exons (coding segments) and introns (non-coding segments). Consequently, a majority of them are multi exon genes (MEG). However, a considerable amount of single exon genes (SEG) are present in the human genome (approximately 12%). This amount is sizeable and it is important to probe their molecular function and cellular role. Hence, we performed a genome wide functional assignment to 3750 SEG sequences using PFAM (protein family database), PROSITE (database of biologically meaningful signatures or motifs) and SUPERFAMILY (a library covering all proteins of known 3 dimensional structure). PFAM assigned 13% SEG to trans-membrane receptor genes of the G-protein coupled receptor (GPCR) family and showed that a majority of SEG proteins have DNA binding function. PROSITE identified 336 unique motif types in them and this accounts for 25% of all known patterns, with a majority having PHOSPHORYLATION and ACETYLATION signals. SUPERFAMILY assigned 33% SEG to the membrane all alpha (proteins containing alpha helix structural elements according to SCOP (structural classification of proteins) definition). Functional assignment of SEG proteins at multiple levels (sequence signals, sequence families, 3D structures) using PFAM, PROSITE and SUPERFAMILY is envisioned to suggest their selective and predominant molecular function in cellular systems. Their function as DNA binding, phosphorylating, acetylating and house-keeping agents is intriguing. The analysis also showed evidence of SEG expression and retro-transposition. However, this information is inadequate to draw concerted conclusion on the prevalent role played by these proteins in cellular biology. A complete understanding of SEG function will help to explore their role in cellular environment. The derived datasets from these analyses are available at http://sege.ntu.edu.sg/wester/intronless/human/.

Effect of ginsenoside Rb1 on rat liver phosphoproteins induced by carbon tetrachloride.

We investigated the effects of ginsenoside Rb1 (G-Rb1), a major saponin from Panax ginseng C. A. MEYER, on rat liver protein phosphorylation after intraperitoneal administration of CCl4 alone or together with G-Rb1. We found that 118, 63, and 34kDa proteins were prominently phosphorylated in liver homogenates prepared from CCl4-administered rats, while these protein-phosphorylations were inhibited in the homogenate prepared from the G-Rb1 plus CCl4-administration group. When inhibitors of protein kinases were exogenously added to the homogenates from either the CCl4-administered group or the G-Rb1 plus CCl4-administered group, their phosphorylations were inhibited much more by W-7, an inhibitor of Ca2+/calmodulin-dependent protein kinase (CaM-PK), than by H-7, an inhibitor of protein kinase C (C-kinase). Interestingly, only 34kDa was phosphorylated in homogenates prepared from the corn oil-, G-Rb1-, and G-Rb1 plus CCl4-administered groups by the exogenous addition of sodium fluoride (NaF), an inhibitor of glycogen synthase. Additionally, G-Rb1 inhibited the Ca(2+)-accumulation induced by CCl4 both in liver homogenates and microsomes. The above results imply that G-Rb1 inhibits the CCl4-induced protein phosphorylations by modulating CaM-PK rather than C-kinase, and that 34kDa protein may play a different biological role in cellular environment from 118 and 63kDa proteins. Therefore, a study in which G-Rb1 is employed as a modulator of critical CCl4-induced phenomena ranging from the disturbance of Ca2+ concentration to protein phosphorylation may be successfully applicable to investigate the diverse physiological functions of liver.