Native state

In biochemistry, the native state of a protein or nucleic acid is its properly folded and/or assembled form, which is operative and functional. The native state of a biomolecule may possess all four levels of biomolecular structure, with the secondary through quaternary structure being formed from weak interactions along the covalently-bonded backbone. This is in contrast to the denatured state, in which these weak interactions are disrupted, leading to the loss of these forms of structure and retaining only the biomolecule's primary structure. Biochemistry Proteins Protein structure While all protein molecules begin as simple unbranched chains of amino acids, once completed they assume highly specific three-dimensional shapes. That ultimate shape, known as tertiary structure, is the folded shape that possesses a minimum of free energy. It is a protein's tertiary, folded structure that makes it capable of performing its biological function. In fact, shape changes

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Protein folding

Protein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologicall

Protein

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing met

Protein tertiary structure

Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the prote

Spatial SPION Localization in Liposome Membranes

Davide Demurtas, Alke Fink

Nanocarriers, including liposomes, offer great opportunities for targeted and controlled therapy. The development in this field has led to a large panel of drug delivery systems, which can be classified into 3 different nanovector generations. However, the success of such smart materials requires the control of a large variety of properties and parameters. Unfortunately, characterization at the nanoscale is often cumbersome and many methods are still being developed. Liposomes have been characterized by cryogenic electron microscopy (CryoTEM) for quite some time, also in combination with nanoparticles, in particular with superparamagnetic iron oxide nanoparticles (SPIONs) incorporated inside the liposomal membrane. CryoTEM, unlike classical TEM, maintains the native state of the liposomes. The quick freezing of the sample immobilizes particles and liposomes exactly at their position in the suspension. Therefore, localization information can be extracted from the images. However, data must be treated extremely carefully keeping in mind that 2-D projections of a 3-D object are observed. In this paper, we discuss the analysis of cryoTEM images of liposome-particle hybrids, including the estimation of the contrast transfer function (CTF) and electron dose, as well as the correct positioning of the sample holder and tomography for accurate localization.

Ieee-Inst Electrical Electronics Engineers Inc2013

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Detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the lack of a comprehensive characterization of the aggregates, which are typically heterogeneous. Here we designed a reporter chaperone substrate, MLucV, composed of a stress-labile luciferase flanked by stress-resistant fluorescent domains, which upon denaturation formed a discrete population of small aggregates. Combining Forster resonance energy transfer and enzymatic activity measurements provided unprecedented details on the aggregated, unfolded, Hsp70-bound and native MLucV conformations. The Hsp70 mechanism first involved ATP-fueled disaggregation and unfolding of the stable pre-aggregated substrate, which stretched MLucV beyond simply unfolded conformations, followed by native refolding. The ATP-fueled unfolding and refolding action of Hsp70 on MLucV aggregates could accumulate native MLucV species under elevated denaturing temperatures highly adverse to the native state. These results unambiguously exclude binding and preventing of aggregation from the non-equilibrium mechanism by which Hsp70 converts stable aggregates into metastable native proteins.

NATURE PORTFOLIO2022

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins

Alessandro Barducci, Paolo De Los Rios, Bruno Claude Daniel Fauvet, Pierre Goloubinoff, Alberto Stefano Sassi

During and after protein translation, molecular chaperones require ATP hydrolysis to favor the native folding of their substrates and, under stress, to avoid aggregation and revert misfolding. Why do some chaperones need ATP, and what are the consequences of the energy contributed by the ATPase cycle? Here, we used biochemical assays and physical modeling to show that the bacterial chaperones GroEL (Hsp60) and DnaK (Hsp70) both use part of the energy from ATP hydrolysis to restore the native state of their substrates, even under denaturing conditions in which the native state is thermodynamically unstable. Consistently with thermodynamics, upon exhaustion of ATP, the metastable native chaperone products spontaneously revert to their equilibrium non-native states. In the presence of ATPase chaperones, some proteins may thus behave as open ATP-driven, nonequilibrium systems whose fate is only partially determined by equilibrium thermodynamics.

2018

PHYS-441: Statistical physics of biomacromolecules

Introduction to the application of the notions and methods of theoretical physics to problems in biology.

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In this course we will study the cell (minimum unit of life) and its components. We will study several key cellular features: Membranes, genomes, channels and receptors. We will apply the laws of physics to develop models to make quantitative and predictive statements.

CH-210: Biochemistry

Les constituants biochimiques de l'organisme, protéines, glucides, lipides, à la lumière de l'évolution des concepts et des progrès en biologie moléculaire et génétique, sont étudiés.