Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm.

The deposition of proteins in the form of amyloid fibrils and plaques is the characteristic feature of more than 20 degenerative conditions affecting either the central nervous system or a variety of peripheral tissues. As these conditions include Alzheimer's, Parkinson's and the prion diseases, several forms of fatal systemic amyloidosis, and at least one condition associated with medical intervention (haemodialysis), they are of enormous importance in the context of present-day human health and welfare. Much remains to be learned about the mechanism by which the proteins associated with these diseases aggregate and form amyloid structures, and how the latter affect the functions of the organs with which they are associated. A great deal of information concerning these diseases has emerged, however, during the past 5 years, much of it causing a number of fundamental assumptions about the amyloid diseases to be re-examined. For example, it is now apparent that the ability to form amyloid structures is not an unusual feature of the small number of proteins associated with these diseases but is instead a general property of polypeptide chains. It has also been found recently that aggregates of proteins not associated with amyloid diseases can impair the ability of cells to function to a similar extent as aggregates of proteins linked with specific neurodegenerative conditions. Moreover, the mature amyloid fibrils or plaques appear to be substantially less toxic than the pre-fibrillar aggregates that are their precursors. The toxicity of these early aggregates appears to result from an intrinsic ability to impair fundamental cellular processes by interacting with cellular membranes, causing oxidative stress and increases in free Ca2+ that eventually lead to apoptotic or necrotic cell death. The 'new view' of these diseases also suggests that other degenerative conditions could have similar underlying origins to those of the amyloidoses. In addition, cellular protection mechanisms, such as molecular chaperones and the protein degradation machinery, appear to be crucial in the prevention of disease in normally functioning living organisms. It also suggests some intriguing new factors that could be of great significance in the evolution of biological molecules and the mechanisms that regulate their behaviour.

http://virtuallaboratory.colorado.edu/Biofundamentals-2014/chapters/Protein%20Aggregation%20and%20toxicity.pdf

Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution

Proteins can exist in a trinity of structures: the ordered state, the molten globule, and the random coil. The five following examples suggest that native protein structure can correspond to any of the three states (not just the ordered state) and that protein function can arise from any of the three states and their transitions. (1) In a process that likely mimics infection, fd phage converts from the ordered into the disordered molten globular state. (2) Nucleosome hyperacetylation is crucial to DNA replication and transcription; this chemical modification greatly increases the net negative charge of the nucleosome core particle. We propose that the increased charge imbalance promotes its conversion to a much less rigid form. (3) Clusterin contains an ordered domain and also a native molten globular region. The molten globular domain likely functions as a proteinaceous detergent for cell remodeling and removal of apoptotic debris. (4) In a critical signaling event, a helix in calcineurin becomes bound and surrounded by calmodulin, thereby turning on calcineurin's serine/threonine phosphatase activity. Locating the calcineurin helix within a region of disorder is essential for enabling calmodulin to surround its target upon binding. (5) Calsequestrin regulates calcium levels in the sarcoplasmic reticulum by binding approximately 50 ions/molecule. Disordered polyanion tails at the carboxy terminus bind many of these calcium ions, perhaps without adopting a unique structure. In addition to these examples, we will discuss 16 more proteins with native disorder. These disordered regions include molecular recognition domains, protein folding inhibitors, flexible linkers, entropic springs, entropic clocks, and entropic bristles. Motivated by such examples of intrinsic disorder, we are studying the relationships between amino acid sequence and order/disorder, and from this information we are predicting intrinsic order/disorder from amino acid sequence. The sequence-structure relationships indicate that disorder is an encoded property, and the predictions strongly suggest that proteins in nature are much richer in intrinsic disorder than are those in the Protein Data Bank. Recent predictions on 29 genomes indicate that proteins from eucaryotes apparently have more intrinsic disorder than those from either bacteria or archaea, with typically > 30% of eucaryotic proteins having disordered regions of length > or = 50 consecutive residues.

Intrinsically Disordered Proteins

In contrast to such “shocks” for which the genome is unprepared, are those a genome must face repeatedly, and for which it is prepared to respond in a programmed manner. Examples are the “heat shock” responses in eukaryotic organisms, and the “SOS” responses in bacteria. Each of these initiates a highly programmed sequence of events within the cell that serves to cushion the effects of the shock. Some sensing mechanism must be present in these instances to alert the cell to imminent danger, and to set in motion the orderly sequence of events that will mitigate this danger. The responses of genomes to unanticipated challenges are not so precisely programmed. Nevertheless, these are sensed, and the genome responds in a discernible but initially unforeseen manner. Barbara McClintock–Nobel lecture , 8 December 1983 These prophetic words by Barbara McClintock eloquently capture the essence of the heat shock response. At the time these words were written, it was known that all organisms shared a common response to physiological stress. Some of the genes encoding heat shock proteins had just been cloned and the basis of heat shock gene regulation was in the early stages of investigation. However, the function of the heat shock response and the role of heat shock proteins were still a mystery. This mystery slowly began to unravel, and by the 1980s, some information on the function of the heat shock proteins as proteases or unfolded polypeptide-binding proteins had already accumulated. These early stages of elucidation of the biochemical...

https://epub.ub.uni-muenchen.de/7685/1/7685.pdf

The Biology of heat shock proteins and molecular chaperones.

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.

/pdf/principles-of-protein-folding-a-perspective-from-simple-3k57kibqjs.pdf

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

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2881%2980642-4

α-lactalbumin: compact state with fluctuating tertiary structure?

The temperature-induced coil-globule transition has been studied in dilute aqueous solutions (with 200 mg/L SDS) for different fractions of poly(N-isopropylacrylamide) (PNIPAM) and poly-(N-isopropylmethacrylamide) (PNIPMAM) using scanning microcalorimetry, diffusion, and size-exclusion chromatography (FPLC). It has been shown that both these polymers undergo a coil-globule transition upon temperature increase. This transition is accompanied by cooperative heat absorption and a decrease of heat capacity, which makes it similar to the cold denaturation of globular proteins. The globule-coil transition is an all-or-none process only for the fractions with the lowest molecular weights (∼10 x 10 3 ) while fractions of larger molecular weights behave as if they consist of quasi-independent cooperative units, the domains. The number of domains in a macromolecule is proportional to the molecular weight of the polymer. This suggests that the domain character of cooperative transitions in large proteins does not, in principle, need evolutionary-selected amino acid sequences but can occur even in homopolymers.

"Domain" Coil-Globule Transition in Homopolymers

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2888%2980485-X

The 'molten globule' state is involved in the translocation of proteins across membranes?

We describe a novel physical state of a protein molecule which is nearly as compact as the native state and has pronounced secondary structure, but differs from the native state by the large increase of thermal fluctuations (in particular, by the large mobility of side groups). This state has been characterized in detail for the acid form of bovine α-lactalbumin as a result of the study of physical properties of this state by a large variety of different methods (hydrodynamics, diffuse X-ray scattering, circular dichroism and infrared spectra, polarization of the luminescence, proton magnetic resonance, deuterium exchange and microcalorimetry). It has been shown that bovine α-lactalbumin can be transformed into a similar state by thermal denaturation. This process is thermodynamically two state (i.e. all-or-none transition), which means that this state differs from the native one by a phase transition of the first order.

Compact state of a protein molecule with pronounced small-scale mobility: bovine alpha-lactalbumin.

The temperature-induced intramolecular coil-globule transition in poly(N-isopropylacrylamide) has been studied by microcalorimetry to investigate the cooperativity of this transition. Measurements were performed in the presence of sodium dodecyl sulfate (SDS) which prevents the polymer from aggregation both in the coil and in the globule state. It has been shown that the effective (van't Hoff) enthalpy of transition of a cooperative unit is 120 times less than the calorimetric enthalpy of a polymer molecule. This means that a coil-globule transition in this polymer is not an «all-or-none» process and occurs independently in cooperative units («domains») which are 120 times smaller than the polymer molecule and have a molecular weight about 6×10 4

V. E. Bychkova

Papers

α-lactalbumin: compact state with fluctuating tertiary structure?

"Domain" Coil-Globule Transition in Homopolymers

The 'molten globule' state is involved in the translocation of proteins across membranes?

Compact state of a protein molecule with pronounced small-scale mobility: bovine alpha-lactalbumin.

Cooperativity of the Coil-Globule Transition in a Homopolymer: Microcalorimetric Study of Poly(N-isopropylacrylamide)