Vladimir Yarov-Yarovoy - Revision history

Jon Sack at 01:35, 23 January 2013

2013-01-23T01:35:24Z

←Older revision		Revision as of 01:35, 23 January 2013
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	Evolution of ion channels from bacteria to human took several billion years and while there are basic features that are common to bacterial and human ion channels, such as pore-forming and/or voltage-sensing domains, there are abundance of unique features in every human ion channel family that are absent in bacterial ion channels and have been designed through evolutionary time to accomplish highly specific functions. My third project is focusing on exploring evolution of human voltage-gated ion channels using available prokaryotic and eukaryotic genomes and high-resolution ion channels structures. Human ion channel family is ranking third in a number of family members after the G protein coupled receptors and the protein kinases. To identify the mechanisms by which historical mutations generated distinct human ion channel functions, it is essential to compare proteins through evolutionary time. Moreover, reconstruction of key intermediate ancestors of ion channels by computational structural design can further advance our understanding of evolution of human ion channel function. Previously, I used bioinformatics based analysis of available high-resolution membrane proteins structures to derive parameters of membrane environment-specific scoring function used in the Rosetta-Membrane method. I now propose to analyze evolution of human voltage-gated sodium channels using phylogenetic trees and multiple sequence alignments of homologous sequences and correlate it with available structural and functional data. I will use the Rosetta-Membrane method to predict structures of human ion channels for which high-resolution structures are not available. Mapping of evolutionary information onto human voltage-gated sodium channel structures will give us significant new insights into evolution of their structure and function.		Evolution of ion channels from bacteria to human took several billion years and while there are basic features that are common to bacterial and human ion channels, such as pore-forming and/or voltage-sensing domains, there are abundance of unique features in every human ion channel family that are absent in bacterial ion channels and have been designed through evolutionary time to accomplish highly specific functions. My third project is focusing on exploring evolution of human voltage-gated ion channels using available prokaryotic and eukaryotic genomes and high-resolution ion channels structures. Human ion channel family is ranking third in a number of family members after the G protein coupled receptors and the protein kinases. To identify the mechanisms by which historical mutations generated distinct human ion channel functions, it is essential to compare proteins through evolutionary time. Moreover, reconstruction of key intermediate ancestors of ion channels by computational structural design can further advance our understanding of evolution of human ion channel function. Previously, I used bioinformatics based analysis of available high-resolution membrane proteins structures to derive parameters of membrane environment-specific scoring function used in the Rosetta-Membrane method. I now propose to analyze evolution of human voltage-gated sodium channels using phylogenetic trees and multiple sequence alignments of homologous sequences and correlate it with available structural and functional data. I will use the Rosetta-Membrane method to predict structures of human ion channels for which high-resolution structures are not available. Mapping of evolutionary information onto human voltage-gated sodium channel structures will give us significant new insights into evolution of their structure and function.
		+
		+
		+	'''''Personal Interests'''''
		+
		+	Contemporary Art http://www.moma.org/
		+
		+	Classical Music http://www.sfsymphony.org/
		+
		+	Contemporary Ballet http://www.linesballet.org/
		+
		+	Contemporary Jazz http://www.esperanzaspalding.com/
		+
		+	http://www.sfjazz.org/
		+
		+	Skiing http://www.skilaketahoe.com/
		+
		+	http://www.northstarattahoe.com/
		+
		+	Trans Music http://www.atb-music.com/
		+
		+	http://www.arminvanbuuren.com/
		+
		+	Interactive 3D environment http://unity3d.com/
		+
		+	Sports http://www.fcbarcelona.com/
		+
		+	http://www.rafaelnadal.com/
		+
		+	http://www.49ers.com/
		+
		+	Wine
		+	http://napavalley.com/
		+
		+	http://www.sonomavalley.com/
		+
		+	http://willamettewines.com/
		+
		+	http://www.washingtonwine.org/wineries/

Jon Sack at 01:16, 23 January 2013

2013-01-23T01:16:29Z

←Older revision		Revision as of 01:16, 23 January 2013
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	{{Template: Sack Lab}}		{{Template: Sack Lab}}
-	~~'''~~''Vladimir Yarov-Yarovoy''~~'''~~	+
		+	== ''Vladimir Yarov-Yarovoy'' ==
		+

	'''''Education'''''		'''''Education'''''
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	Department of Biochemistry and Molecular Medicine, University of California,		Department of Biochemistry and Molecular Medicine, University of California,
	Davis, California.		Davis, California.
-
-	~~'''''Awards and Honors'''''~~
-
-	~~1998 Biophysical Society graduate student travel award.~~
-
-	~~2003-2009 NIH Research Career Development Award.~~
-
-	~~2008-2009 University of Washington Royalty Research Fund Award.~~

	'''''Professional Organizations'''''		'''''Professional Organizations'''''

Jon Sack at 01:12, 23 January 2013

2013-01-23T01:12:37Z

←Older revision		Revision as of 01:12, 23 January 2013
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	{{Template: Sack Lab}}		{{Template: Sack Lab}}
		+	'''''Vladimir Yarov-Yarovoy'''''
		+
	'''''Education'''''		'''''Education'''''

Jon Sack at 01:10, 23 January 2013

2013-01-23T01:10:51Z

←Older revision		Revision as of 01:10, 23 January 2013
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		+	'''''Education'''''
		+
		+	1985-1993 Master of Science (M.S.) Degree in Physics, Department of Physics, Moscow
		+	State University, Moscow, Russia.
		+
		+	1993-1998 Doctor of Philosophy (Ph.D.) Degree in Biochemistry and Molecular Biology,
		+	Department of Environmental and Biomolecular Systems, OGI School of Science
		+	& Engineering, Oregon Health Science University, Portland, Oregon.
		+
		+	1999-2003 Senior Fellow in Computational Biology and Biophysics. Supervisors: Dr. David
		+	Baker, Professor, Department of Biochemistry, and Dr. William A. Catterall,
		+	Professor and Chairman, Department of Pharmacology, University of
		+	Washington, Seattle, Washington.
		+
		+	'''''Faculty Positions Held'''''
		+
		+	2003-2004 Acting Instructor. Department of Pharmacology, University of Washington,
		+	Seattle, Washington.
		+
		+	2004-2006 Acting Assistant Professor. Department of Pharmacology, University of
		+	Washington, Seattle, Washington.
		+
		+	2006-2010 Research Assistant Professor. Department of Pharmacology, University of
		+	Washington, Seattle, Washington.
		+
		+	2011-present Assistant Professor. Department of Physiology and Membrane Biology,
		+	Department of Biochemistry and Molecular Medicine, University of California,
		+	Davis, California.
		+
		+	'''''Awards and Honors'''''
		+
		+	1998 Biophysical Society graduate student travel award.
		+
		+	2003-2009 NIH Research Career Development Award.
		+
		+	2008-2009 University of Washington Royalty Research Fund Award.
		+
		+	'''''Professional Organizations'''''
		+
		+	Member of the American Pain Society
		+
		+	Member of the Biophysical Society
		+
		+	'''''Research Interests'''''
		+
		+	My research interests and expertise encompass neuroscience, protein structure, computational biology, and evolution. Main focus of my research group is on structure and function studies of voltage-gated ion channels, computational design and chemical synthesis of subtype-specific modulators of voltage-gated ion channels, development of computational methods for membrane protein structure prediction and design, and analysis of evolution of human voltage-gated ion channels.
		+
		+	Function and modulation of neuronal sodium channels are critical for the neuromodulation of electrical excitability and synaptic transmission in neurons - the basis for many aspects of signal transduction, learning, memory and physiological regulation. Mutations in neuronal voltage-gated sodium channel genes are responsible for various human neurological disorders. Furthermore, human neuronal voltage-gated sodium channels are primary targets of therapeutic drugs used as local anesthetics and for treatment of neurological and cardiac disorders. My first project is focusing on studying of neuronal voltage-gated sodium channels structure, function, and modulation in order to design new therapeutically useful drugs for treatment of pain and epilepsy. Serious, chronic pain affects at least 116 million Americans each year and epilepsy affects nearly 3 million Americans and 50 million people Worldwide. However, the treatment of chronic pain and epilepsy remains a major unmet medical need because the use of currently available drugs is limited due to incomplete efficacy and/or significant side effects. Considerable efforts by pharmaceutical industry toward identifying selective inhibitors of one or more of Nav channel subtypes did not generate any genuinely subtype selective blockers and none are currently advancing through clinical trials. My laboratory uses an innovative approach to design novel subtype selective Nav channel blocking drugs with high efficacy and minimum side effects. Novel drugs will be tested using methods of electrophysiology, biochemistry, and molecular biology. This project will provide key structural information on the molecular basis of neuronal voltage-gated sodium channels function and its interaction with therapeutically useful subtype-specific modulators. Understanding of function and modulation of the neuronal voltage-gated sodium channels on structural level will give us profound insights into the fundamental mechanisms underlying neuromodulation and signal transduction
		+
		+	Over the past decade, there has been significant progress in determining membrane protein structures in general and ion channel structures in particular using x-ray crystallography methods. However, it is still very difficult to obtain high-resolution structural information about these proteins. My second project is focusing on further development of the Rosetta-Membrane computational method for high-resolution membrane protein structure prediction and design. I developed the original Rosetta-Membrane method for membrane protein structure prediction in collaboration with David Baker's group at the University of Washington and applied it for modeling of membrane proteins in general and ion channels in particular. I now propose to further improve accuracy of the Rosetta-Membrane method and expand its capabilities to design membrane proteins with new functions.
		+
		+	Evolution of ion channels from bacteria to human took several billion years and while there are basic features that are common to bacterial and human ion channels, such as pore-forming and/or voltage-sensing domains, there are abundance of unique features in every human ion channel family that are absent in bacterial ion channels and have been designed through evolutionary time to accomplish highly specific functions. My third project is focusing on exploring evolution of human voltage-gated ion channels using available prokaryotic and eukaryotic genomes and high-resolution ion channels structures. Human ion channel family is ranking third in a number of family members after the G protein coupled receptors and the protein kinases. To identify the mechanisms by which historical mutations generated distinct human ion channel functions, it is essential to compare proteins through evolutionary time. Moreover, reconstruction of key intermediate ancestors of ion channels by computational structural design can further advance our understanding of evolution of human ion channel function. Previously, I used bioinformatics based analysis of available high-resolution membrane proteins structures to derive parameters of membrane environment-specific scoring function used in the Rosetta-Membrane method. I now propose to analyze evolution of human voltage-gated sodium channels using phylogenetic trees and multiple sequence alignments of homologous sequences and correlate it with available structural and functional data. I will use the Rosetta-Membrane method to predict structures of human ion channels for which high-resolution structures are not available. Mapping of evolutionary information onto human voltage-gated sodium channel structures will give us significant new insights into evolution of their structure and function.

Daniel Clay Austin at 03:35, 13 December 2012

2012-12-13T03:35:33Z

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2012-10-03T22:31:13Z

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