A new view of protein folding kinetics replaces the idea of ‘folding pathways’ with the broader notions of energy landscapes and folding funnels. New experiments are needed to explore them.

From Levinthal to pathways to funnels

Nearly 100 proteins are known to be regulated by hsp90. Most of these substrates or "client proteins" are involved in signal transduction, and they are brought into complex with hsp90 by a multiprotein hsp90/hsp70-based chaperone machinery. In addition to binding substrate proteins at the chaperone site(s), hsp90 binds cofactors at other sites that are part of the heterocomplex assembly machinery as well as immunophilins that connect assembled substrate*hsp90 complexes to protein-trafficking systems. In the 5 years since we last reviewed this subject, much has been learned about hsp90 structure, nucleotide-binding, and cochaperone interactions; the most important concept is that ATP hydrolysis by an intrinsic ATPase activity results in a conformational change in hsp90 that is required to induce conformational change in a substrate protein. The conformational change induced in steroid receptors is an opening of the steroid-binding cleft so that it can be accessed by steroid. We have now developed a minimal system of five purified proteins-hsp90, hsp70, Hop, hsp40, and p23- that assembles stable receptor*hsp90 heterocomplexes. An hsp90*Hop*hsp70*hsp40 complex opens the cleft in an ATP-dependent process to produce a receptor*hsp90 heterocomplex with hsp90 in its ATP-bound conformation, and p23 then interacts with the hsp90 to stabilize the complex. Stepwise assembly experiments have shown that hsp70 and hsp40 first interact with the receptor in an ATP-dependent reaction to produce a receptor*hsp70*hsp40 complex that is "primed" to be activated to the steroid-binding state in a second ATP-dependent step with hsp90, Hop, and p23. Successful use of the five-protein system with other substrates indicates that it can assemble signal protein*hsp90 heterocomplexes whether the substrate is a receptor, a protein kinase, or a transcription factor. This purified system should facilitate understanding of how eukaryotic hsp70 and hsp90 work together as essential components of a process that alters the conformations of substrate proteins to states that respond in signal transduction.

Regulation of signaling protein function and trafficking by the hsp90/hsp70-based chaperone machinery.

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.

Pigments are present in all living matter and provide attractive colors and play basic roles in the development of organisms. Human beings, like most animals, come in contact with their surroundings through color, and things can or cannot be acceptable based on their color characteristics. This review presents the basic information about pigments focusing attention on the natural ones; it emphasizes the principal plant pigments: carotenoids, anthocyanins, and betalains. Special considerations are given to their salient characteristics; to their biosynthesis, taking into account the biochemical and molecular biology information generated in their elucidation; and to the processing and stability properties of these compounds as food colorants.

Natural Pigments: Carotenoids, Anthocyanins, and Betalains — Characteristics, Biosynthesis, Processing, and Stability

https://people.unica.it/flaminiacesaremarincola/files/2011/12/Analisi-StrutturaProteina-Review.pdf

Spectroscopic methods for analysis of protein secondary structure.

Lipocalin-type Prostaglandin D Synthase (β-Trace) Is a Newly Recognized Type of Retinoid Transporter

High helical propensity of the peptide fragments derived from beta-lactoglobulin, a predominantly beta-sheet protein.

A simple procedure is described for synthesis of oligonucleotides by phosphate chemistry. Chains can be constructed rapidly with minimal equipment (a syringe and reagent bottles). The method is illustrated by synthesis of d-TGCAGGTT. Pertinent supporting data on the effect of variations in the detritylation, condensation, oxidation, capping and cleavage steps in the synthetic approach and in isolation procedures are also presented.

Syringe method for stepwise chemical synthesis of oligonucleotides

http://www-vendruscolo.ch.cam.ac.uk/hamada09jmb.pdf

Competition between Folding, Native-State Dimerisation and Amyloid Aggregation in β-Lactoglobulin

Coiled coils, which mediate the associations and regulate the functions of various proteins, have a representative amino acid sequence of (defgabc)n heptad repeats and usually have hydrophobic residues at the a and d positions. We have designed a triple-stranded parallel α-helical coiled coil, in which the amino acid sequence is YGG(IEKKIEA)4. To construct a peptide that undergoes metal ion induced self-assembly into a triple-stranded coiled coil, we engineered a metal binding site in the hydrophobic core of the coiled coil. We replaced two Ile residues of the third heptad with His residues. The peptide had a random structure in aqueous solution. In contrast, in the presence of a transition metal ion, the peptide exhibited an α-helical conformation. The metal-complexed peptide was triple stranded and had a parallel orientation, as determined by sedimentation equilibrium and fluorescence quenching analyses. Metal ion titrations monitored by circular dichroism revealed that the dissociation constants, Kd, w...

Toshiki Tanaka

Papers

Lipocalin-type Prostaglandin D Synthase (β-Trace) Is a Newly Recognized Type of Retinoid Transporter

High helical propensity of the peptide fragments derived from beta-lactoglobulin, a predominantly beta-sheet protein.

Syringe method for stepwise chemical synthesis of oligonucleotides

Competition between Folding, Native-State Dimerisation and Amyloid Aggregation in β-Lactoglobulin

Metal Ion Induced Self-Assembly of a Designed Peptide into a Triple-Stranded α-Helical Bundle: A Novel Metal Binding Site in the Hydrophobic Core