• New advances in the protein folding proc

    From ScienceDaily@1:317/3 to All on Wed Mar 23 22:30:44 2022
    New advances in the protein folding process thermodynamics
    Optical tweezers to unravel the complexity of living matter

    Date:
    March 23, 2022
    Source:
    University of Barcelona
    Summary:
    In biophysics, the kinetic states of molecules play a determining
    role in the metabolic and physiological processes in which they take
    part. Now, a new article specifies for the first time the levels of
    energy, the entropy and the enthalpy of protein folding. To do so,
    the team used a device with optical tweezers that enables changing
    the experimental temperature between 5-oC and 40-oC.



    FULL STORY ==========================================================================
    In biophysics, the kinetic states of molecules play a determining role in
    the metabolic and physiological processes in which they take part. Now,
    a paper published in the journal Proceedings of the National Academy
    of Sciences(PNAS) specifies for the first time the levels of energy,
    the entropy and the enthalpy of protein folding. To do so, the team used
    a device with optical tweezers that enables changing the experimental temperature between 5-oC and 40-oC.


    ==========================================================================
    The study was led by Professor Fe`lix Ritort, from the Faculty of Physics
    and the Institute of Nanosciences and Nanotechnology of the University
    of Barcelona (IN2UB). Its first author is the researcher Marc Rico-Pasto
    (UB) and it counts with the collaboration of teams from the University of Padova (Italy), the Institute of Bioengineering in Lausanne (Switzerland)
    and the company SpliceBio, whose headquarters are in the Barcelona
    Science Park (PCB).

    Optical tweezers to unravel the complexity of living matter The emergence
    of innovative techniques such as optical and magnetic tweezers has revolutionized research in biophysics, and specifically, the study of thermodynamic properties in macromolecules: proteins, nucleic acids,
    etc. This type of technology enables the manipulation of individual
    molecules with nanometre precision (10-9 meters) applying forces in
    the piconewton range (10- 12 newtons). Therefore, researchers can
    characterize the thermodynamic properties of complex biomolecules with unprecedented resolution. The application of such techniques provides with
    new scenarios for the experimental studies in the field of thermodynamics
    from a statistical approach, an interpretation of thermodynamics that
    was only possible from a theoretical perspective to date.

    However, these techniques have limitations that prevent researchers
    from differentiating the origins of the measured forces. At the moment, combining different techniques to expand the number of control parameters
    is a challenge in biophysics. This is precisely what the team in charge
    of this study has done: introducing a temperature monitor in the optical tweezers to determine, for the first time, the entropy and enthalpy of
    protein folding.

    Energy landscapes in protein folding During the folding process of
    proteins and other macromolecules, different kinetic states take place
    between the native state and the denatured state.

    Examples are transition states, molecular intermediates and misfolded structures, which have a transient nature that makes thermodynamical characterization more difficult in experiments with a high number
    of molecules -- from the 1023 molecule order, the value known as the
    Avogadro's number - - which are analysed simultaneously. Particularly
    relevant to protein folding are transition states due to their extremely
    short lifetime.

    "Our results reveal that, during the transition state, the protein
    skeletal structure is already built. However, most of the van der Waals interactions - - weak forces -- among the residues are not stabilized,"
    notes Professor Fe`lix Ritort, member of the Department of Condensed
    Matter Physics of the UB.

    "Conclusions show that protein folding can be understood as a process
    defined by two steps. In the first one, the protein reaches the
    transition state in which the native skeletal structure is built, and
    water is expelled from the inside of the polypeptide chain," continues
    Ritort. "In the second step, the protein collapses, the interactions
    between protein residues are stabilized, and the protein reaches the
    native state," concludes the researcher.

    A first reading of the results reveals that there is a change of enthalpy
    and entropy during the transition state corresponding to 20% approximately
    of the total measured in the folding. "This phenomenon shows that the
    protein skeletal structure requires a 20% of the interactions between
    residues. The reading we make from the protein folding goes in line with
    the most recent hypotheses in the field of protein folding," notes Marc Rico-Pasto, also member of the Department of Condensed Matter Physics.

    Despite having stated that the protein skeletal structure is built during
    the transition state, authors say that they cannot conclude the amount
    of native interactions that exist in this state. "We can make a first estimation -- they say -- , but quantifying this result requires some experimental variable that allows us to measure or identify the number
    of bonds built during the molecular folding in real time." The team
    led by Professor Fe`lix Ritort, head of the Small Biosystems Lab of the
    Faculty of Physics, made significant contributions to the study of the thermodynamic properties of complex systems in biomolecules. In previous studies, the team used the model of the barnase protein -- a globular biomolecule secreted by Bacillus amyloliquefaciens -- separated by a
    transition state. The barnase, which does not show intermediate states
    with a lifetime of more than a millisecond during the folding, is also
    the reference model for the characterization method of transition states
    during the protein folding process (phi-value analysis).


    ========================================================================== Story Source: Materials provided by University_of_Barcelona. Note:
    Content may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Marc Rico-Pasto, Annamaria Zaltron, Sebastian J. Davis, Silvia
    Frutos,
    Felix Ritort. Molten globule-like transition state of protein
    barnase measured with calorimetric force spectroscopy. Proceedings
    of the National Academy of Sciences, 2022; 119 (11) DOI:
    10.1073/pnas.2112382119 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/03/220323101224.htm

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