General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics-fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse.

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Principles of protein folding--a perspective from simple exact models.

Charge density-dependent strength of hydration and biological structure

Protein aggregation: folding aggregates, inclusion bodies and amyloid

Understanding protein non-folding.

The folding of most newly synthesized proteins in the cell requires the interaction of a variety of protein cofactors known as molecular chaperones. These molecules recognize and bind to nascent polypeptide chains and partially folded intermediates of proteins, preventing their aggregation and misfolding. There are several families of chaperones; those most involved in protein folding are the 40-kDa heat shock protein (HSP40; DnaJ), 60-kDa heat shock protein (HSP60; GroEL), and 70-kDa heat shock protein (HSP70; DnaK) families. The availability of high-resolution structures has facilitated a more detailed understanding of the complex chaperone machinery and mechanisms, including the ATP-dependent reaction cycles of the GroEL and HSP70 chaperones. For both of these chaperones, the binding of ATP triggers a critical conformational change leading to release of the bound substrate protein. Whereas the main role of the HSP70/HSP40 chaperone system is to minimize aggregation of newly synthesized proteins, the HSP60 chaperones also facilitate the actual folding process by providing a secluded environment for individual folding molecules and may also promote the unfolding and refolding of misfolded intermediates.

https://www.physiology.org/doi/pdf/10.1152/physrev.1999.79.2.425

Chaperone-Mediated Protein Folding

Recently there has been growing recognition of the existence and importance of compact intermediate states of proteins. Such species have been observed under both transient (refolding kinetics) and equilibrium conditions. It is clear that for many proteins most denaturing conditions do not lead to a fully unfolded protein (random coil), but rather to species with substantial secondary structure and substantial compactness, relative to the fully unfolded state. In addition, there is now good experimental data to demonstrate the existence of two classes of compact denatured states of proteins: compact intermediates, in the thermodynamic sense (i.e., a minimum in the free energy profile for the reaction), and compact substates of the unfolded state (Palleros et al., 1993). It is important to note that it is often experimentally difficult to distinguish between these two types of compact denatured states, especially by spectral methods. Recent reviews of compact denatured states, and particularly the molten globule, include those of Dill and Shortle (1991), Ptitsyn (1987, 1992), Kuwajima (1989), Christensen and Pain (1991), and Baldwin and Roder (1991). Theoretical models for the existence of two classes of denatured states have been presented by Dill and co-workers (Alonso et al., 1991), Ptitsyn (1987, 1992), and Finkelstein and Shakhnovich (1989).

Compact Intermediate States in Protein Folding

Oxidative stress and aggregation of the presynaptic protein alpha-synuclein (alpha-Syn) are implied in the pathogenesis of Parkinson's disease and several other neurodegenerative diseases. Various posttranslational modifications, such as oxidation, nitration and truncation, have significant effects on the kinetics of alpha-Syn fibrillation in vitro. alpha-Syn is a typical natively unfolded protein, which possesses some residual structure. The existence of long-range intra-molecular interactions between the C-terminal tail (residues 120-140) and the central part of alpha-Syn (residues 30-100) was recently established (Bertoncini et al. (2005) Proc Natl Acad Sci U S A 102, 1430-1435). Since alpha-Syn has four methionines, two of which (Met 1 and 5) are at the N-terminus and the other two (Met 116 and 127) are in the hydrophobic cluster at the C-terminus of protein, the perturbation of these residues via their oxidation represents a good model for studying the effect of long-range interaction on alpha-Syn fibril formation. In this paper we show that Met 1, 116, and 127 are more protected from the oxidation than Met 5 likely due to the residual structure in the natively unfolded alpha-Syn. In addition to the hydrophobic interactions between the C-terminal hydrophobic cluster and hydrophobic central region of alpha-Syn, there are some long-range electrostatic interactions in this protein. Both of these interactions likely serve as auto-inhibitors of alpha-Syn fibrillation. Methionine oxidation affects both electrostatic and hydrophobic long-range interactions in alpha-Syn. Finally, oxidation of methionines by H2O2 greatly inhibited alpha-Syn fibrillation in vitro, leading to the formation of relatively stable oligomers, which are not toxic to dopaminergic and GABAergic neurons.

Methionine Oxidation Stabilizes Non-Toxic Oligomers of alpha-synuclein through Strengthening the Auto-inhibitory Intra-molecular Long-range Interactions

Epidemiological, population-based case–control, and experimental studies at the molecular, cellular, and organism levels revealed that exposure to various environmental agents, including a number of structurally different agrochemicals, may contribute to the pathogenesis of Parkinson’s disease (PD) and several other neurodegenerative disorders. The role of genetic predisposition in PD has also been increasingly acknowledged, driven by the identification of a number of disease-related genes [e.g., α-synuclein, parkin, DJ-1, ubiquitin C-terminal hydrolase isozyme L1 (UCH-L1), and nuclear receptor-related factor 1]. Therefore, the etiology of this multifactorial disease is likely to involve both genetic and environmental factors. Various neurotoxicants, including agrochemicals, have been shown to elevate the levels of α-synuclein expression in neurons and to promote aggregation of this protein in vivo. Many agrochemicals physically interact with α-synuclein and accelerate the fibrillation and aggregation rates of this protein in vitro. This review analyzes some of the aspects linking α-synuclein to PD, provides brief structural and functional descriptions of this important protein, and represents some data connecting exposure to agrochemicals with α-synuclein aggregation and PD pathogenesis.

Agrochemicals, α-synuclein, and Parkinson's disease.

Recent reports give strong support to the idea that amyloid fibril formation and the subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. In this review recent findings are surveyed to illustrate that protein fibrillogenesis requires a partially folded conformation. This amyloidogenic conformation is relatively unfolded, and shares many structural properties with the premolten globule state, a partially folded intermediate frequently observed in the early stages of protein folding and under some equilibrium conditions. The inherent flexibility of such an intermediate is essential in allowing the conformational rearrangements necessary to form the core cross-β; structure of the amyloid fibril.

Structural and Conformational Prerequisites of Amyloidogenesis

α-Synuclein, a natively unfolded protein aggregation which is implicated in the pathogenesis of Parkinson’s disease and several other neurodegenerative diseases, is known to interact with a great number of unrelated proteins. Some of these proteins, such as β-synuclein and DJ-1, were shown to inhibit α-synuclein aggregation in vitro and in vivo therefore acting as chaperones. Since calbindin-D28K is co-localized with Ca2+ neuronal membrane pumps, and since α-synuclein is also found in the membrane proximity, these two proteins can potentially interact in vivo. Here we show that calbindin-D28K interacts with α-synuclein and inhibits its fibrillation in a calcium-dependent manner, therefore potentially acting as a calcium-dependent chaperone.

Anthony L. Fink

Papers

Compact Intermediate States in Protein Folding

Methionine Oxidation Stabilizes Non-Toxic Oligomers of alpha-synuclein through Strengthening the Auto-inhibitory Intra-molecular Long-range Interactions

Agrochemicals, α-synuclein, and Parkinson's disease.

Structural and Conformational Prerequisites of Amyloidogenesis

Calbindin-D28K acts as a calcium-dependent chaperone suppressing α-synuclein fibrillation in vitro