Post by skyship on Jan 24, 2014 18:46:57 GMT -5
Rebuilding the Proteins, as Carnicom has said:
Summary
Principal Investigator: Wah Chiu
Affiliation: Baylor College of Medicine
Country: USA
Abstract: DESCRIPTION (application abstract):
The chaperonin TRiC is a protein folding nanomachine necessary for the growth of all eukaryotic cells. The protein substrates of this barrel-shaped 16-subunit nanomachine include actins, tubulins, and tumor suppressor proteins. Similarly to its archaeal homolog Mm-cpn, it couples ATP hydrolysis to internalization, folding, and release of newly synthesized polypeptide chains.
The folding cycle includes opening and closing of a built-in lid of the chaperonin critical for binding and release. Our Nanomedicine Development Center (NDC) will extend and integrate the current techniques in electron cryomicroscopy, single-molecule imaging, computational biology, and X-ray crystallography to quantify the chaperonin subunit conformations and dynamics as well as the protein folding intermediates bound within the chaperonin cavity.
The marriage of these advanced technologies will allow us to visualize chaperonin machinery functioning not only in vitro but also within cells. Building on a more comprehensive and quantitative description of these protein folding nanomachines, we will engineer modified chaperonins to provide a novel therapeutic tool for inhibiting and promoting the folding of selected proteins whose misfolding or aggregation are associated with human diseases.
These proteins include actin, tumor suppressor proteins p53 and Von Hippel Lindau, the aggregating A-beta peptide and the cataract related lens protein, gamma-crystallin. Through visualizing conformations and sites in which these chains are folded by the chaperonin, together with their experimentally observed and computed dynamics, we will also design novel substrates that will be folded efficiently in the naturally occurring or newly engineered chaperonin, opening new avenues in protein design.
The corresponding approaches will include design of adaptor peptides for modifying the substrates or chaperonins to enhance or inhibit substrate-chaperone interactions. We have assembled a team of 15 investigators from 6 institutions with expertise in chaperones, protein folding, electron cryomicroscopy, computer simulation and modeling, X-ray crystallography, singlemolecule imaging and trapping, and clinical research. We will work together in developing a strategic set of experimental and computational tools that will enable characterization of biological nanomachines, both in vitro and in vivo.
We will interact with complementary expertise of other NDC in synthetic chemistry and fluorescence technologies. Our Center can be a critical resource to other NDC who need assistance in solving protein folding and aggregation problems. Our clinical investigators will contribute to the design of pilot studies for therapeutic applications in cell culture models of disease states. We also plan new educational tools via virtual courses in design and application of biological nanomachines, aimed at bridging the gap between biology and mechanical engineering for students in our 6 participating institutions. Finally, the organization, collaborations and communications in our NDC exemplify the 21st century goal of conducting interdisciplinary research via new mechanisms of data sharing and analysis.
Funding Period: 2004-09-30 - 2010-09-29
more information: NIH RePORT
Top Publications
ncbi Structural biology of cellular machines
Wah Chiu
National Center for Macromolecular Imaging and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Trends Cell Biol 16:144-50. 2006
ncbi Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel
Irina I Serysheva
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 105:9610-5. 2008
ncbi Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies
Friedrich Förster
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158, USA
J Mol Biol 382:1089-106. 2008
ncbi A role for confined water in chaperonin function
Jeremy L England
James H Clark Center, S297, Stanford University, Stanford, California 94305, USA
J Am Chem Soc 130:11838-9. 2008
ncbi Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility
Mariana Babor
California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158 2330, USA
Proteins 75:846-58. 2009
ncbi The structural dynamics of macromolecular processes
Daniel Russel
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158 2330, USA
Curr Opin Cell Biol 21:97-108. 2009
ncbi Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly
Keren Lasker
Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
J Mol Biol 388:180-94. 2009
ncbi Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy
Yao Cong
National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
Structure 17:749-58. 2009
ncbi Refinement of protein structures into low-resolution density maps using rosetta
Frank DiMaio
Department of Biochemistry, University of Washington, Seattle, 98195, USA
J Mol Biol 392:181-90. 2009
ncbi An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome
Friedrich Förster
Department of Structural Biology, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
Biochem Biophys Res Commun 388:228-33. 2009
www.labome.org/grant/pn2/ey/center/for/center-for-protein-folding-machinery--rmi--7293531.html
We are getting closer, to this cellular machine.
Skyship
Summary
Principal Investigator: Wah Chiu
Affiliation: Baylor College of Medicine
Country: USA
Abstract: DESCRIPTION (application abstract):
The chaperonin TRiC is a protein folding nanomachine necessary for the growth of all eukaryotic cells. The protein substrates of this barrel-shaped 16-subunit nanomachine include actins, tubulins, and tumor suppressor proteins. Similarly to its archaeal homolog Mm-cpn, it couples ATP hydrolysis to internalization, folding, and release of newly synthesized polypeptide chains.
The folding cycle includes opening and closing of a built-in lid of the chaperonin critical for binding and release. Our Nanomedicine Development Center (NDC) will extend and integrate the current techniques in electron cryomicroscopy, single-molecule imaging, computational biology, and X-ray crystallography to quantify the chaperonin subunit conformations and dynamics as well as the protein folding intermediates bound within the chaperonin cavity.
The marriage of these advanced technologies will allow us to visualize chaperonin machinery functioning not only in vitro but also within cells. Building on a more comprehensive and quantitative description of these protein folding nanomachines, we will engineer modified chaperonins to provide a novel therapeutic tool for inhibiting and promoting the folding of selected proteins whose misfolding or aggregation are associated with human diseases.
These proteins include actin, tumor suppressor proteins p53 and Von Hippel Lindau, the aggregating A-beta peptide and the cataract related lens protein, gamma-crystallin. Through visualizing conformations and sites in which these chains are folded by the chaperonin, together with their experimentally observed and computed dynamics, we will also design novel substrates that will be folded efficiently in the naturally occurring or newly engineered chaperonin, opening new avenues in protein design.
The corresponding approaches will include design of adaptor peptides for modifying the substrates or chaperonins to enhance or inhibit substrate-chaperone interactions. We have assembled a team of 15 investigators from 6 institutions with expertise in chaperones, protein folding, electron cryomicroscopy, computer simulation and modeling, X-ray crystallography, singlemolecule imaging and trapping, and clinical research. We will work together in developing a strategic set of experimental and computational tools that will enable characterization of biological nanomachines, both in vitro and in vivo.
We will interact with complementary expertise of other NDC in synthetic chemistry and fluorescence technologies. Our Center can be a critical resource to other NDC who need assistance in solving protein folding and aggregation problems. Our clinical investigators will contribute to the design of pilot studies for therapeutic applications in cell culture models of disease states. We also plan new educational tools via virtual courses in design and application of biological nanomachines, aimed at bridging the gap between biology and mechanical engineering for students in our 6 participating institutions. Finally, the organization, collaborations and communications in our NDC exemplify the 21st century goal of conducting interdisciplinary research via new mechanisms of data sharing and analysis.
Funding Period: 2004-09-30 - 2010-09-29
more information: NIH RePORT
Top Publications
ncbi Structural biology of cellular machines
Wah Chiu
National Center for Macromolecular Imaging and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Trends Cell Biol 16:144-50. 2006
ncbi Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel
Irina I Serysheva
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 105:9610-5. 2008
ncbi Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies
Friedrich Förster
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158, USA
J Mol Biol 382:1089-106. 2008
ncbi A role for confined water in chaperonin function
Jeremy L England
James H Clark Center, S297, Stanford University, Stanford, California 94305, USA
J Am Chem Soc 130:11838-9. 2008
ncbi Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility
Mariana Babor
California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158 2330, USA
Proteins 75:846-58. 2009
ncbi The structural dynamics of macromolecular processes
Daniel Russel
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158 2330, USA
Curr Opin Cell Biol 21:97-108. 2009
ncbi Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly
Keren Lasker
Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
J Mol Biol 388:180-94. 2009
ncbi Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy
Yao Cong
National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
Structure 17:749-58. 2009
ncbi Refinement of protein structures into low-resolution density maps using rosetta
Frank DiMaio
Department of Biochemistry, University of Washington, Seattle, 98195, USA
J Mol Biol 392:181-90. 2009
ncbi An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome
Friedrich Förster
Department of Structural Biology, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
Biochem Biophys Res Commun 388:228-33. 2009
www.labome.org/grant/pn2/ey/center/for/center-for-protein-folding-machinery--rmi--7293531.html
We are getting closer, to this cellular machine.
Skyship