The Experts below are selected from a list of 303 Experts worldwide ranked by ideXlab platform
Donald C Rau - One of the best experts on this subject based on the ideXlab platform.
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role of amino acid insertions on intermolecular forces between arginine peptide condensed dna helices implications for protamine dna packaging in sperm
Biophysical Journal, 2012Co-Authors: Jason E Derouchey, Donald C RauAbstract:In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. We have previously observed that the net attraction between salmon protamine condensed DNA helices was much smaller for DNA condensed by the equivalent homo-arginine peptide. We hypothesized that this is caused by the neutral amino acids present in protamines. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines. The component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance have been determined by the osmotic stress technique coupled with x-ray scattering as a function of the chemistry, position, and number of the amino acid inserted. Neutral amino acids inserted into hexa-arginine increase the short-range repulsion; while only slightly decreasing the longer-ranged attraction. The decrease in net attraction between salmon protamine condensed helices compared with arginine homopeptides can be well explained by amino acid content alone. Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both these observation have biological implications for protamine-DNA packaging in sperm heads.
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role of amino acid insertions on intermolecular forces between arginine peptide condensed dna helices implications for protamine dna packaging in sperm
Journal of Biological Chemistry, 2011Co-Authors: Jason E Derouchey, Donald C RauAbstract:In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines. We have previously observed that the neutral amino acids in salmon protamine decrease the net attraction between protamine-DNA helices compared with the equivalent homo-arginine peptide. Using osmotic stress coupled with x-ray scattering, we have investigated the component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance as a function of the chemistry, position, and number of the amino acid inserted. Neutral amino acids inserted into hexa-arginine increase the short range repulsion while only slightly affecting longer range attraction. The amino acid content alone of salmon protamine is enough to rationalize the forces that package DNA in sperm heads. Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both of these observations have biological implications for protamine-DNA packaging in sperm heads.
David E. Clapham - One of the best experts on this subject based on the ideXlab platform.
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histone phosphorylation by trpm6 s cleaved kinase attenuates adjacent arginine methylation to regulate gene expression
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Grigory Krapivinsky, Luba Krapivinsky, Ana Santacruz, Yunona Manasian, Nora E Renthal, David E. ClaphamAbstract:TRPM6 and TRPM7 are members of the melastatin-related transient receptor potential (TRPM) subfamily of ion channels. Deletion of either gene in mice is embryonically lethal. TRPM6/7 are the only known examples of single polypeptides containing both an ion channel pore and a serine/threonine kinase (chanzyme). Here we show that the C-terminal kinase domain of TRPM6 is cleaved from the channel domain in a cell type-specific fashion and is active. Cleavage requires that the channel conductance is functional. The cleaved kinase translocates to the nucleus, where it is strictly localized and phosphorylates specific histone serine and threonine (S/T) residues. TRPM6-cleaved kinases (M6CKs) bind subunits of the protein arginine methyltransferase 5 (PRMT5) molecular complex that make important epigenetic modifications by methylating histone arginine residues. Histone phosphorylation by M6CK results in a dramatic decrease in methylation of arginines adjacent to M6CK-phosphorylated amino acids. Knockout of TRPM6 or inactivation of its kinase results in global changes in histone S/T phosphorylation and changes the transcription of hundreds of genes. We hypothesize that M6CK associates with the PRMT5 molecular complex in the nucleus, directing M6CK to a specific genomic location and providing site-specific histone phosphorylation. M6CK histone phosphorylation, in turn, regulates transcription by attenuating the effect of local arginine methylation.
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Histone phosphorylation by TRPM6’s cleaved kinase attenuates adjacent arginine methylation to regulate gene expression
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Grigory Krapivinsky, Luba Krapivinsky, Yunona Manasian, Ana Santa-cruz, Nora E Renthal, David E. ClaphamAbstract:TRPM6 and TRPM7 are members of the melastatin-related transient receptor potential (TRPM) subfamily of ion channels. Deletion of either gene in mice is embryonically lethal. TRPM6/7 are the only known examples of single polypeptides containing both an ion channel pore and a serine/threonine kinase (chanzyme). Here we show that the C-terminal kinase domain of TRPM6 is cleaved from the channel domain in a cell type-specific fashion and is active. Cleavage requires that the channel conductance is functional. The cleaved kinase translocates to the nucleus, where it is strictly localized and phosphorylates specific histone serine and threonine (S/T) residues. TRPM6-cleaved kinases (M6CKs) bind subunits of the protein arginine methyltransferase 5 (PRMT5) molecular complex that make important epigenetic modifications by methylating histone arginine residues. Histone phosphorylation by M6CK results in a dramatic decrease in methylation of arginines adjacent to M6CK-phosphorylated amino acids. Knockout of TRPM6 or inactivation of its kinase results in global changes in histone S/T phosphorylation and changes the transcription of hundreds of genes. We hypothesize that M6CK associates with the PRMT5 molecular complex in the nucleus, directing M6CK to a specific genomic location and providing site-specific histone phosphorylation. M6CK histone phosphorylation, in turn, regulates transcription by attenuating the effect of local arginine methylation.
Grigory Krapivinsky - One of the best experts on this subject based on the ideXlab platform.
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histone phosphorylation by trpm6 s cleaved kinase attenuates adjacent arginine methylation to regulate gene expression
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Grigory Krapivinsky, Luba Krapivinsky, Ana Santacruz, Yunona Manasian, Nora E Renthal, David E. ClaphamAbstract:TRPM6 and TRPM7 are members of the melastatin-related transient receptor potential (TRPM) subfamily of ion channels. Deletion of either gene in mice is embryonically lethal. TRPM6/7 are the only known examples of single polypeptides containing both an ion channel pore and a serine/threonine kinase (chanzyme). Here we show that the C-terminal kinase domain of TRPM6 is cleaved from the channel domain in a cell type-specific fashion and is active. Cleavage requires that the channel conductance is functional. The cleaved kinase translocates to the nucleus, where it is strictly localized and phosphorylates specific histone serine and threonine (S/T) residues. TRPM6-cleaved kinases (M6CKs) bind subunits of the protein arginine methyltransferase 5 (PRMT5) molecular complex that make important epigenetic modifications by methylating histone arginine residues. Histone phosphorylation by M6CK results in a dramatic decrease in methylation of arginines adjacent to M6CK-phosphorylated amino acids. Knockout of TRPM6 or inactivation of its kinase results in global changes in histone S/T phosphorylation and changes the transcription of hundreds of genes. We hypothesize that M6CK associates with the PRMT5 molecular complex in the nucleus, directing M6CK to a specific genomic location and providing site-specific histone phosphorylation. M6CK histone phosphorylation, in turn, regulates transcription by attenuating the effect of local arginine methylation.
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Histone phosphorylation by TRPM6’s cleaved kinase attenuates adjacent arginine methylation to regulate gene expression
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Grigory Krapivinsky, Luba Krapivinsky, Yunona Manasian, Ana Santa-cruz, Nora E Renthal, David E. ClaphamAbstract:TRPM6 and TRPM7 are members of the melastatin-related transient receptor potential (TRPM) subfamily of ion channels. Deletion of either gene in mice is embryonically lethal. TRPM6/7 are the only known examples of single polypeptides containing both an ion channel pore and a serine/threonine kinase (chanzyme). Here we show that the C-terminal kinase domain of TRPM6 is cleaved from the channel domain in a cell type-specific fashion and is active. Cleavage requires that the channel conductance is functional. The cleaved kinase translocates to the nucleus, where it is strictly localized and phosphorylates specific histone serine and threonine (S/T) residues. TRPM6-cleaved kinases (M6CKs) bind subunits of the protein arginine methyltransferase 5 (PRMT5) molecular complex that make important epigenetic modifications by methylating histone arginine residues. Histone phosphorylation by M6CK results in a dramatic decrease in methylation of arginines adjacent to M6CK-phosphorylated amino acids. Knockout of TRPM6 or inactivation of its kinase results in global changes in histone S/T phosphorylation and changes the transcription of hundreds of genes. We hypothesize that M6CK associates with the PRMT5 molecular complex in the nucleus, directing M6CK to a specific genomic location and providing site-specific histone phosphorylation. M6CK histone phosphorylation, in turn, regulates transcription by attenuating the effect of local arginine methylation.
Michael E. Green - One of the best experts on this subject based on the ideXlab platform.
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The Role of Proton Transport in Gating Current in a Voltage Gated Ion Channel, as Shown by Quantum Calculations
MDPI AG, 2018Co-Authors: Alisher M. Kariev, Michael E. GreenAbstract:Over two-thirds of a century ago, Hodgkin and Huxley proposed the existence of voltage gated ion channels (VGICs) to carry Na+ and K+ ions across the cell membrane to create the nerve impulse, in response to depolarization of the membrane. The channels have multiple physiological roles, and play a central role in a wide variety of diseases when they malfunction. The first channel structure was found by MacKinnon and coworkers in 1998. Subsequently, the structure of a number of VGICs was determined in the open (ion conducting) state. This type of channel consists of four voltage sensing domains (VSDs), each formed from four transmembrane (TM) segments, plus a pore domain through which ions move. Understanding the gating mechanism (how the channel opens and closes) requires structures. One TM segment (S4) has an arginine in every third position, with one such segment per domain. It is usually assumed that these arginines are all ionized, and in the resting state are held toward the intracellular side of the membrane by voltage across the membrane. They are assumed to move outward (extracellular direction) when released by depolarization of this voltage, producing a capacitive gating current and opening the channel. We suggest alternate interpretations of the evidence that led to these models. Measured gating current is the total charge displacement of all atoms in the VSD; we propose that the prime, but not sole, contributor is proton motion, not displacement of the charges on the arginines of S4. It is known that the VSD can conduct protons. Quantum calculations on the Kv1.2 potassium channel VSD show how; the key is the amphoteric nature of the arginine side chain, which allows it to transfer a proton. This appears to be the first time the arginine side chain has had its amphoteric character considered. We have calculated one such proton transfer in detail: this proton starts from a tyrosine that can ionize, transferring to the NE of the third arginine on S4; that arginine’s NH then transfers a proton to a glutamate. The backbone remains static. A mutation predicted to affect the proton transfer has been qualitatively confirmed experimentally, from the change in the gating current-voltage curve. The total charge displacement in going from a normal closed potential of −70 mV across the membrane to 0 mV (open), is calculated to be approximately consistent with measured values, although the error limits on the calculation require caution in interpretation
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Cys Mutation + MTS Caution is Needed in Interpretation of Arg Reaction in the S4 Transmembrane Segment of a Voltage Sensing Domain (VSD) of a Voltage Gated Channel: Results of Quantum Calculations
Biophysical Journal, 2014Co-Authors: Alisher M. Kariev, Michael E. GreenAbstract:In all previous work on voltage gated channels, mutation of the arginines on the S4 segment of the VSD, then reaction with an MTS reagent, followed by channel shutdown, has been taken to mean that the arginine was exposed on the surface from which the reagent was applied. This may require more care in interpretation. Cysteine is smaller than the arginine by about the size of the reactive sulfonate on the MTS; The mutation leaves a large cavity where the arginine side chain had been, so the MTS can reach the cysteine, possibly via the omega pore. The backbone atoms need not move. The distance between S4 and S2 or S3 remains largely unchanged. Salt bridges, (e.g., R297-E183) however, are disturbed; when cysteine is in the reactive (negative) form, it constitutes a charge reversal mutation, as the arginine was (presumably) positive. Quantum calculations on configurations of this region for R300C of the VSD of Kv1.2 show that the cys anion can fold away from the cavity where it could react, in a manner dependent on the water and protons present. See the preprint posted at http://arxiv.org/abs/1309.1373. Optimizations have been done at BLYP/6-31G∗∗ level. Acknowledgement: Computations were done at the Brookhaven National Laboratory CFN cluster, and the CUNY hpc facility.
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A possible role for phosphate in complexing the arginines of S4 in voltage gated channels.
Journal of Theoretical Biology, 2004Co-Authors: Michael E. GreenAbstract:Abstract Phosphate ions are known to complex guanidinium groups, which are the side chains of arginine. Voltage gated channels that allow passage of ions through cell membranes, producing, for example the nerve impulse, are in many cases composed of four domains, each with six transmembrane segments. The S4 transmembrane segments of these channels have arginines placed in such a way that they would be expected to complex phosphate. Known phosphate–arginine complexes are reasonably strong. Here, an ab initio calculation reinforces the expectation that a strong complex could form. As a consequence, if the S4 moved, it would carry either no charge, or at most half of what is expected from fully charged arginines. This suggests that it may be necessary to rethink voltage gating models in which the gating current is produced by physical motion of the S4 transmembrane segments.
Jason E Derouchey - One of the best experts on this subject based on the ideXlab platform.
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role of amino acid insertions on intermolecular forces between arginine peptide condensed dna helices implications for protamine dna packaging in sperm
Biophysical Journal, 2012Co-Authors: Jason E Derouchey, Donald C RauAbstract:In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. We have previously observed that the net attraction between salmon protamine condensed DNA helices was much smaller for DNA condensed by the equivalent homo-arginine peptide. We hypothesized that this is caused by the neutral amino acids present in protamines. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines. The component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance have been determined by the osmotic stress technique coupled with x-ray scattering as a function of the chemistry, position, and number of the amino acid inserted. Neutral amino acids inserted into hexa-arginine increase the short-range repulsion; while only slightly decreasing the longer-ranged attraction. The decrease in net attraction between salmon protamine condensed helices compared with arginine homopeptides can be well explained by amino acid content alone. Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both these observation have biological implications for protamine-DNA packaging in sperm heads.
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role of amino acid insertions on intermolecular forces between arginine peptide condensed dna helices implications for protamine dna packaging in sperm
Journal of Biological Chemistry, 2011Co-Authors: Jason E Derouchey, Donald C RauAbstract:In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines. We have previously observed that the neutral amino acids in salmon protamine decrease the net attraction between protamine-DNA helices compared with the equivalent homo-arginine peptide. Using osmotic stress coupled with x-ray scattering, we have investigated the component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance as a function of the chemistry, position, and number of the amino acid inserted. Neutral amino acids inserted into hexa-arginine increase the short range repulsion while only slightly affecting longer range attraction. The amino acid content alone of salmon protamine is enough to rationalize the forces that package DNA in sperm heads. Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both of these observations have biological implications for protamine-DNA packaging in sperm heads.
