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  • richardmitnick 12:41 pm on September 6, 2012 Permalink | Reply
    Tags: , , , , , Molecular Foundry at Berkeley Lab   

    From Berkeley Lab: “Forcing the Molecular Bond Issue” 


    Berkeley Lab

    New and Improved Model of Molecular Bonding from Researchers at Berkeley Lab’s Molecular Foundry

    September 05, 2012
    Lynn Yarris

    Material properties and interactions are largely determined by the binding and unbinding of their constituent molecules, but the standard model used to interpret data on the formation and rupturing of molecular bonds suffers from inconsistencies. A collaboration of researchers led by a scientist at the U.S Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) has developed a first-of-its-kind model for providing a comprehensive description of the way in which molecular bonds form and rupture. This model enables researchers to predict the ‘binding free energy’ of a given molecular system, which is key to predicting how that molecule will interact with other molecules.

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    Under dynamic force spectroscopy, the bonds of a molecular system are subjected to controlled stretching until the bonds break. (Image courtesy of Jim DeYoreo, Berkeley Lab)

    ‘Molecular binding and unbinding events are much simpler than we have been led to believe from the standard model over the past decade,’ says Jim DeYoreo, a scientist with the Molecular Foundry, a DOE nanoscience center at Berkeley Lab who was one of the leaders of this research. ‘With our new model, we now have a clear means for measuring one of the most important parameters governing how materials and molecules bind together.'”

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 7:46 pm on February 21, 2012 Permalink | Reply
    Tags: , , , , Molecular Foundry at Berkeley Lab,   

    From Berkeley Lab: “How Good Cholesterol Turns Bad” 


    Berkeley Lab

    Berkeley Lab Researchers Find New Evidence on How Cholesterol Gets Moved from HDLs to LDLs

    February 21, 2012
    Lynn Yarris

    “Researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have found new evidence to explain how cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol from ‘good’ high density lipoproteins (HDLs) to ‘bad’ low density lipoproteins (LDLs). These findings point the way to the design of safer, more effective next generation CETP inhibitors that could help prevent the development of heart disease.

    Gang Ren, a materials physicist and electron microscopy expert with Berkeley Lab’s Molecular Foundry, a DOE nanoscience research center, led a study in which the first structural images of CETP interacting with HDLs and LDLs were recorded. The images and structural analyses support the hypothesis that cholesterol is transferred from HDLs to LDLs via a tunnel running through the center of the CETP molecule.

    ‘Our images show that CETP is a small (53 kilodaltons) banana-shaped asymmetric molecule with a tapered N-terminal domain and a globular C-terminal domain,’ Ren says. ‘We discovered that the CETP’s N-terminal penetrates HDL and its C-terminal interacts with LDL forming a ternary complex. Structure analyses lead us to hypothesize that the interaction may generate molecular forces that twist the terminals, creating pores at both ends of the CETP. These pores connect with central cavities in the CETP to form a tunnel that serves as a conduit for the movement of cholesterol from the HDL.'”

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    (1) CETP penetrates HDL to its cholesterol core. (2) Upon interaction with LDL/VLDL, molecular forces cause the formation of pores at either end of CETP. (3) These pores connect with CETP’s central cavities to form a tunnel for the transfer of cholesterol to LDL/VLDL, which (4) reduces HDL in size. (No image credit)

    See the full and very important article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 5:58 am on January 25, 2012 Permalink | Reply
    Tags: , , , , , Molecular Foundry at Berkeley Lab   

    From Berkeley Lab: “Under the Electron Microscope – A 3-D Image of an Individual Protein” 


    Berkeley Lab

    The high resolution of Lawrence Berkeley National Laboratory’s Gang Ren

    Sabin Russell
    JANUARY 24, 2012

    “When Gang Ren whirls the controls of his cryo-electron microscope, he compares it to fine-tuning the gearshift and brakes of a racing bicycle. But this machine at the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) is a bit more complex. It costs nearly $1.5 million, operates at the frigid temperature of liquid nitrogen, and it is allowing scientists to see what no one has seen before.

    At the Molecular Foundry, Berkeley Lab’s acclaimed nanotechnology research center, Ren has pushed his Zeiss Libra 120 Cryo-Tem microscope to resolutions never envisioned by its German manufacturers, producing detailed snapshots of individual molecules. Today, he and his colleague Lei Zhang are reporting the first 3-D images of an individual protein ever obtained with enough clarity to determine its structure.”

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    3-D images from a single particle (A) a series of images of an ApoA-1 protein particle, taken from different angles as indicated. A succession of four computer enhancements (projections) clarifies the signal. In the right column is the 3-D image compiled from the clarified data. B) is a close-up of the reconstructed 3-D image. C) Analysis shows how the particle structure is formed by three ApoA-1 proteins (red, green, blue noodle-like models)

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    Staff scientist Gang Ren (standing) and is postdoc colleague Lei Zhang can checking images of individual proteins from their cryo-electron microscope at Berkeley Lab’s Molecular Foundry.

    See the full article here.

    A US Department of Energy National Laboratory Operated by the University of California

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