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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