Research overview - Revision history

imported>Guentert: /* Applications */

2011-03-21T13:17:13Z

Applications

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	* Analysis of the role of water molecules in specific protein-DNA recognition in one of the earliest nanosecond molecular dynamics simulations of a protein-DNA complex ([[Publications#Billeter96\|Billeter et al. 1996]]).		* Analysis of the role of water molecules in specific protein-DNA recognition in one of the earliest nanosecond molecular dynamics simulations of a protein-DNA complex ([[Publications#Billeter96\|Billeter et al. 1996]]).

	* NMR studies of two Alzheimer peptides with widely different plaque-competence, Aβ(1–40)ox and Aβ(1–40)ox~~, showing~~ that there are no significant conformational differences between their monomeric forms in water ([[Publications#Riek01\|Riek et al. 2001]])		* NMR studies of two Alzheimer peptides with widely different plaque-competence, Aβ(1–40)ox and Aβ(1–40)ox showed that there are no significant conformational differences between their monomeric forms in water ([[Publications#Riek01\|Riek et al. 2001]])

	* Structural studies of metallothioneins, proteins containing Zn or Cd clusters ([[Publications#Riek99\|Riek et al. 1999]], [[Publications#Peroza09\|Peroza et al. 2009]])		* Structural studies of metallothioneins, proteins containing Zn or Cd clusters ([[Publications#Riek99\|Riek et al. 1999]], [[Publications#Peroza09\|Peroza et al. 2009]])

	* Structure-guided fragment-based in silico drug design of dengue protease inhibitors ([[Publications#Knehans11\|Knehans et al. 2011]])		* Structure-guided fragment-based in silico drug design of dengue protease inhibitors ([[Publications#Knehans11\|Knehans et al. 2011]])

imported>Guentert: /* Applications */

2011-03-21T13:16:30Z

Applications

← Older revision		Revision as of 13:16, 21 March 2011
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	* Conformational stability and activity of p73 require a second helix in the tetramerization domain ([[Publications#Coutandin09\|Coutandin et al. 2009]])		* Conformational stability and activity of p73 require a second helix in the tetramerization domain ([[Publications#Coutandin09\|Coutandin et al. 2009]])

	* Elucidation of an intramolecular regulation mechanism for pheromone binding and release by the Bombyx mori pheromone-binding protein ([[Publications#Horst01\|Horst et al. 2001]], [[Publications#Lee02\|Lee et al. 2002]]).		* Elucidation of an intramolecular regulation mechanism for pheromone binding and release by the ''Bombyx mori'' pheromone-binding protein ([[Publications#Horst01\|Horst et al. 2001]], [[Publications#Lee02\|Lee et al. 2002]]).

	* Structures of the Na,K-ATPase nucleotide-binding domain free and in complex with ATP ([[Publications#Hilge03\|Hilge et al. 2003]])		* Structures of the Na,K-ATPase nucleotide-binding domain free and in complex with ATP ([[Publications#Hilge03\|Hilge et al. 2003]])

imported>Guentert: /* Applications */

2011-03-21T13:15:57Z

Applications

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	* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.		* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.

	* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses~~, determining~~ 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).		* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses that has determined 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).

	* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).		* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).

imported>Guentert: /* Applications */

2011-03-21T13:15:25Z

Applications

← Older revision		Revision as of 13:15, 21 March 2011
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	* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.		* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.

	* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses ~~(2002–2007)~~, determining 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).		* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses, determining 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).

	* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).		* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).

imported>Guentert: /* Experimental techniques */

2011-03-21T13:14:11Z

Experimental techniques

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	Computational methods have also been important in the development of new experimental techniques that allow the study of biomolecular systems that have so far been impossible or difficult to analyze:		Computational methods have also been important in the development of new experimental techniques that allow the study of biomolecular systems that have so far been impossible or difficult to analyze:

	* Optimal stereo- and regiospecific isotope labeling of amino acids (stereo-array isotope labeling; [http://www.sailnmr.org/SAIL]), which yielded the NMR solution structure of the 41 kDa maltodextrin-binding protein MBP. This is the first solution structure determination of a protein larger than 30 kDa using detailed experimental information on the side-chains ([[Publications#Kainosho06_1\|Kainosho et al. 2006]]).		* Optimal stereo- and regiospecific isotope labeling of amino acids (stereo-array isotope labeling; [http://www.sailnmr.org/ SAIL]), which yielded the NMR solution structure of the 41 kDa maltodextrin-binding protein MBP. This is the first solution structure determination of a protein larger than 30 kDa using detailed experimental information on the side-chains ([[Publications#Kainosho06_1\|Kainosho et al. 2006]]).

	* Structure determination of proteins in living cells ([[Publications#Sakakibara09\|Sakakibara et al. 2009]], [[Publications#Ikeya10\|Ikeya et al. 2010]]).		* Structure determination of proteins in living cells ([[Publications#Sakakibara09\|Sakakibara et al. 2009]], [[Publications#Ikeya10\|Ikeya et al. 2010]]).

imported>Guentert: /* Software development */

2011-03-21T13:13:26Z

Software development

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	== Software development ==		== Software development ==

	The abovementioned algorithmic developments have been implemented in a number of [[Software\|softwares]]. Many of these are widely used in academic and industrial research.		The abovementioned algorithmic developments have been implemented in a number of [[Software\|softwares]]. Many of these are widely used in academic and industrial research.


	== Experimental techniques ==		== Experimental techniques ==

imported>Guentert at 13:12, 21 March 2011

2011-03-21T13:12:55Z

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	Our research experience is in the field of computational methodology for molecular systems, with an emphasis on algorithmic developments for studying the structure and dynamics of proteins using computational methods in conjunction with data from experiments, e.g. by NMR spectroscopy. Today most NMR protein structures are solved using algorithms and software that have been developed by the group and its present and former coworkers.		Our research experience is in the field of computational methodology for molecular systems, with an emphasis on algorithmic developments for studying the structure and dynamics of proteins using computational methods in conjunction with data from experiments, e.g. by NMR spectroscopy. Today most NMR protein structures are solved using algorithms and software that have been developed by the group and its present and former coworkers.

	~~Research achievements include:~~

	== Algorithmic developments for computer-aided chemistry/structural biology ==		== Algorithmic developments for computer-aided chemistry/structural biology ==

imported>Guentert: /* Computational methods development for the analysis of experimental data */

2011-03-21T13:10:56Z

Computational methods development for the analysis of experimental data

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	* The software package [[PROSA]] for NMR data processing ([[Publications#Güntert92_2\|Güntert et al. 1992]]), and methods for automatic baseline correction ([[FLATT]], [[IFLAT]]) and the measurements of scalar couplings ([[INFIT]]).		* The software package [[PROSA]] for NMR data processing ([[Publications#Güntert92_2\|Güntert et al. 1992]]), and methods for automatic baseline correction ([[FLATT]], [[IFLAT]]) and the measurements of scalar couplings ([[INFIT]]).

	* The first generally applicable algorithm for automated NMR chemical shift assignment ([[Publications#Bartels96\|Bartels et al. 1996]], [[Publications#Bartels97\|Bartels et al.]]), a crucial and difficult step of NMR spectrum interpretation. The algorithm, [[GARANT]], can use any combination of spectra as input data and determines assignments by searching for an optimal matching between expected and observed peaks using a genetic algorithm combined with local optimization.		* The first generally applicable algorithm for automated NMR chemical shift assignment ([[Publications#Bartels96\|Bartels et al. 1996]], [[Publications#Bartels97\|Bartels et al. 1997]]), a crucial and difficult step of NMR spectrum interpretation. The algorithm, [[GARANT]], can use any combination of spectra as input data and determines assignments by searching for an optimal matching between expected and observed peaks using a genetic algorithm combined with local optimization.

	* Widely used computational tools for interactive and semi-automated NMR spectrum analysis ([[EASY]], [[XEASY]], [[KUJIRA]]).		* Widely used computational tools for interactive and semi-automated NMR spectrum analysis ([[EASY]], [[XEASY]], [[KUJIRA]]).

imported>Mickey: /* Applications */

2011-03-21T13:01:51Z

Applications

imported>Mickey: /* Experimental techniques */

2011-03-21T12:59:10Z

Experimental techniques

← Older revision		Revision as of 12:59, 21 March 2011
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	Computational methods have also been important in the development of new experimental techniques that allow the study of biomolecular systems that have so far been impossible or difficult to analyze:		Computational methods have also been important in the development of new experimental techniques that allow the study of biomolecular systems that have so far been impossible or difficult to analyze:

	* Optimal stereo- and regiospecific isotope labeling of amino acids (stereo-array isotope labeling; [http://www.sailnmr.org/SAIL]), which yielded the NMR solution structure of the 41 kDa maltodextrin-binding protein MBP. This is the first solution structure determination of a protein larger than 30 kDa using detailed experimental information on the side-chains ([[Publications#Kainosho06_1\|Kainosho et al. 2006]])		* Optimal stereo- and regiospecific isotope labeling of amino acids (stereo-array isotope labeling; [http://www.sailnmr.org/SAIL]), which yielded the NMR solution structure of the 41 kDa maltodextrin-binding protein MBP. This is the first solution structure determination of a protein larger than 30 kDa using detailed experimental information on the side-chains ([[Publications#Kainosho06_1\|Kainosho et al. 2006]]).

	* Structure determination of proteins in living cells ([[Publications#Sakakibara09\|Sakakibara et al. 2009]], [[Publications#Ikeya10\|Ikeya et al. 2010]])		* Structure determination of proteins in living cells ([[Publications#Sakakibara09\|Sakakibara et al. 2009]], [[Publications#Ikeya10\|Ikeya et al. 2010]]).

	* Transmembrane segment enhanced labeling for the backbone assignment of helical membrane proteins ([[Publications#Reckel08\|Reckel et al. 2008]])		* Transmembrane segment enhanced labeling for the backbone assignment of helical membrane proteins ([[Publications#Reckel08\|Reckel et al. 2008]])

← Older revision		Revision as of 13:17, 21 March 2011
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	* Analysis of the role of water molecules in specific protein-DNA recognition in one of the earliest nanosecond molecular dynamics simulations of a protein-DNA complex ([[Publications#Billeter96\|Billeter et al. 1996]]).		* Analysis of the role of water molecules in specific protein-DNA recognition in one of the earliest nanosecond molecular dynamics simulations of a protein-DNA complex ([[Publications#Billeter96\|Billeter et al. 1996]]).

	* NMR studies of two Alzheimer peptides with widely different plaque-competence, Aβ(1–40)ox and Aβ(1–40)ox~~, showing~~ that there are no significant conformational differences between their monomeric forms in water ([[Publications#Riek01\|Riek et al. 2001]])		* NMR studies of two Alzheimer peptides with widely different plaque-competence, Aβ(1–40)ox and Aβ(1–40)ox showed that there are no significant conformational differences between their monomeric forms in water ([[Publications#Riek01\|Riek et al. 2001]])

	* Structural studies of metallothioneins, proteins containing Zn or Cd clusters ([[Publications#Riek99\|Riek et al. 1999]], [[Publications#Peroza09\|Peroza et al. 2009]])		* Structural studies of metallothioneins, proteins containing Zn or Cd clusters ([[Publications#Riek99\|Riek et al. 1999]], [[Publications#Peroza09\|Peroza et al. 2009]])

	* Structure-guided fragment-based in silico drug design of dengue protease inhibitors ([[Publications#Knehans11\|Knehans et al. 2011]])		* Structure-guided fragment-based in silico drug design of dengue protease inhibitors ([[Publications#Knehans11\|Knehans et al. 2011]])

← Older revision		Revision as of 13:16, 21 March 2011
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	* Conformational stability and activity of p73 require a second helix in the tetramerization domain ([[Publications#Coutandin09\|Coutandin et al. 2009]])		* Conformational stability and activity of p73 require a second helix in the tetramerization domain ([[Publications#Coutandin09\|Coutandin et al. 2009]])

	* Elucidation of an intramolecular regulation mechanism for pheromone binding and release by the Bombyx mori pheromone-binding protein ([[Publications#Horst01\|Horst et al. 2001]], [[Publications#Lee02\|Lee et al. 2002]]).		* Elucidation of an intramolecular regulation mechanism for pheromone binding and release by the ''Bombyx mori'' pheromone-binding protein ([[Publications#Horst01\|Horst et al. 2001]], [[Publications#Lee02\|Lee et al. 2002]]).

	* Structures of the Na,K-ATPase nucleotide-binding domain free and in complex with ATP ([[Publications#Hilge03\|Hilge et al. 2003]])		* Structures of the Na,K-ATPase nucleotide-binding domain free and in complex with ATP ([[Publications#Hilge03\|Hilge et al. 2003]])

← Older revision		Revision as of 13:15, 21 March 2011
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	* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.		* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.

	* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses~~, determining~~ 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).		* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses that has determined 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).

	* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).		* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).

← Older revision		Revision as of 13:15, 21 March 2011
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	* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.		* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.

	* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses ~~(2002–2007)~~, determining 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).		* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses, determining 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).

	* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).		* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).

← Older revision		Revision as of 13:01, 21 March 2011
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	* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.		* [[Protein structures\|NMR solution structures of more than 40 proteins]], including those listed below, and others.

	* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses (2002–2007), determining 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]])		* Participation in the “Protein 3000 Project”, the Japanese National Project on Protein Structural and Functional Analyses (2002–2007), determining 3000 new protein structures. More than half of them were solved using the CYANA software (e.g., [[Publications#Pantoja-Uceda04\|Pantoja-Uceda et al. 2004]], [[Publications#López-Méndez04\|López-Méndez et al. 2004]], [[Publications#Nameki04\|Nameki et al. 2004]], [[Publications#Scott04\|Scott et al. 2004]], [[Publications#Pantoja-Uceda05\|Pantoja-Uceda et al. 2005]], [[Publications#Nameki05\|Nameki et al. 2005]], [[Publications#Scott05\|Scott et al. 2005]], [[Publications#Li05\|Li et al. 2005]], [[Publications#Hamada06\|Hamada et al. 2006]], [[Publications#Kuwasako06\|Kuwasako et al. 2006]], [[Publications#Ohnishi07\|Ohnishi et al. 2007]], [[Publications#Kobayashi07\|Kobayashi et al. 2007]], [[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Lin08\|Lin et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#He09_2\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#He09_3\|He et al. 2009]], [[Publications#He10\|He et al. 2010]], [[Publications#Handa10\|Handa et al. 2010]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]]).

	* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).		* Structure determination of integral membrane proteins: OmpX ([[Publications#Fernández04\|Fernández et al. 2004]]), the C-terminal catalytic fragment of presenilin 1 ([[Publications#Sobhanifar10\|Sobhanifar et al. 2010]]), and bacteriorhodopsin (unpublished).

	* Structures of various mammalian prion proteins that are involved in transmissible spongiform encephalopathies such as BSE or the human Creutzfeldt-Jakob disease ([[Publications#Calzolai00\|Calzolai et al. 2000]], [[Publications#Zahn03\|Zahn et al. 2003]], [[Publications#Calzolai05\|Calzolai et al. 2005]], [[Publications#Lysek05\|Lysek et al. 2005]])		* Structures of various mammalian prion proteins that are involved in transmissible spongiform encephalopathies such as BSE or the human Creutzfeldt-Jakob disease ([[Publications#Calzolai00\|Calzolai et al. 2000]], [[Publications#Zahn03\|Zahn et al. 2003]], [[Publications#Calzolai05\|Calzolai et al. 2005]], [[Publications#Lysek05\|Lysek et al. 2005]]).

	* Atomic resolution structure of the fungal prion protein FgHET-s(218-289) in amyloid fibrils determined by solid state NMR (unpublished).		* Atomic resolution structure of the fungal prion protein FgHET-s(218-289) in amyloid fibrils determined by solid state NMR (unpublished).

	* Structural basis for the selectivity of the external thioesterase of the surfactin non-ribosomal peptide synthetase ([[Publications#Koglin08\|Koglin et al. 2008]])		* Structural basis for the selectivity of the external thioesterase of the surfactin non-ribosomal peptide synthetase ([[Publications#Koglin08\|Koglin et al. 2008]]).

	* Structural basis for specific protein-RNA recognition ([[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]])		* Structural basis for specific protein-RNA recognition ([[Publications#Kuwasako08_1\|Kuwasako et al. 2008]], [[Publications#Kuwasako08_2\|Kuwasako et al. 2008]], [[Publications#Nagata08\|Nagata et al. 2008]], [[Publications#Ohnishi09\|Ohnishi et al. 2009]], [[Publications#He09_1\|He et al. 2009]], [[Publications#Tsuda09\|Tsuda et al. 2009]], [[Publications#Yamashita11\|Yamashita et al. 2011]], [[Publications#Tsuda11\|Tsuda et al. 2011]])
Line 83:		Line 83:
	* Structures of the Na,K-ATPase nucleotide-binding domain free and in complex with ATP ([[Publications#Hilge03\|Hilge et al. 2003]])		* Structures of the Na,K-ATPase nucleotide-binding domain free and in complex with ATP ([[Publications#Hilge03\|Hilge et al. 2003]])

	* NMR structures of the periplasmic chaperones CcmE ([[Publications#Enggist02\|Enggist et al. 2002]]) and FimC ([[Publications#Pellecchia98_1\|Pellecchia et al. 1998]], [[Publications#Pellecchia98_2\|Pellecchia et al. 1998]])		* NMR structures of the periplasmic chaperones CcmE ([[Publications#Enggist02\|Enggist et al. 2002]]) and FimC ([[Publications#Pellecchia98_1\|Pellecchia et al. 1998]], [[Publications#Pellecchia98_2\|Pellecchia et al. 1998]]).

	* NMR solution structures of the calreticulin P-domain ([[Publications#Ellgaard01\|Ellgaard et al. 2001]], [[Publications#Ellgaard02\|Ellgaard et al. 2002]])		* NMR solution structures of the calreticulin P-domain ([[Publications#Ellgaard01\|Ellgaard et al. 2001]], [[Publications#Ellgaard02\|Ellgaard et al. 2002]]).

	* Analysis of the role of water molecules in specific protein-DNA recognition in one of the earliest nanosecond molecular dynamics simulations of a protein-DNA complex ([[Publications#Billeter96\|Billeter et al. 1996]])		* Analysis of the role of water molecules in specific protein-DNA recognition in one of the earliest nanosecond molecular dynamics simulations of a protein-DNA complex ([[Publications#Billeter96\|Billeter et al. 1996]]).

	* NMR studies of two Alzheimer peptides with widely different plaque-competence, Aβ(1–40)ox and Aβ(1–40)ox, showing that there are no significant conformational differences between their monomeric forms in water ([[Publications#Riek01\|Riek et al. 2001]])		* NMR studies of two Alzheimer peptides with widely different plaque-competence, Aβ(1–40)ox and Aβ(1–40)ox, showing that there are no significant conformational differences between their monomeric forms in water ([[Publications#Riek01\|Riek et al. 2001]])