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. 2017 Jan 17;50(1):105-111.
doi: 10.1021/acs.accounts.6b00511. Epub 2016 Dec 29.

How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway

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How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway

H Jane Dyson et al. Acc Chem Res. .

Abstract

Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (∼2 s) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ∼ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the conformational ensembles formed in the presence of denaturing agents and low pH can be characterized as models for the unfolded states of the protein. Newer NMR techniques such as measurement of residual dipolar couplings in the various partly folded states, and relaxation dispersion measurements to probe invisible states present at low concentrations, have contributed to providing a detailed picture of the apomyoglobin folding pathway. The research summarized in this Account was aimed at characterizing and comparing the equilibrium and kinetic intermediates both structurally and dynamically, as well as delineating the complete folding pathway at a residue-specific level, in order to answer the question: "What is it about the amino acid sequence that causes each molecule in the unfolded protein ensemble to start folding, and, once started, to proceed towards the formation of the correctly folded three-dimensional structure?"

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Figures

Figure 1
Figure 1
Ribbon diagram of the backbone of sperm whale myoglobin showing helices A (red), B (orange), C (yellow), D (green), E (turquoise), F (blue), G (purple) and H (pink). The Trp 14 side chain is shown in its position opposite Gly 73 in the wild-type protein Reproduced with permission from ref.. Copyright 2005 Elsevier. The figure was prepared using Molmol.
Figure 2
Figure 2
Sequence variation of the average area buried upon folding (AABUF) for the myoglobin sequence, plotted using a nine-residue moving average. Black curve: wild-type sperm whale sequence. Red dotted curve: sperm whale sequence with the two mutations W14G, G73W Reproduced with permission from ref.. Copyright 2005 Elsevier.
Figure 3
Figure 3
Residue-specific plot of proton occupancy in the burst phase intermediate, measured at 6.4 ms folding time in a urea-jump folding experiment, with varying durations of the pH 10.1 labeling pulse. A. wild-type apomyoglobin. B. W14G, G73W mutant apomyoglobin. Red: pulse duration 7 ms; orange, 12 ms; green, 20 ms; blue, 35 ms; purple, 65 ms. The locations of helices A–H are shown Reproduced with permission from ref.. Copyright 2005 Elsevier.
Figure 4
Figure 4
Schematic diagram of the apomyoglobin folding pathway. The AABUF profile (top of figure) shows peaks where the amino acid sequence indicates local clusters of hydrophobic residues and side chains such as Lys and Glu that contain long aliphatic regions in their side chains. Local interactions between the G and H helices and transient long-range interactions between the A and G/H regions are observed in the acid-unfolded state. The molten globule intermediate Ia is the first observable state, with stabilized helical structure and patterns of protected amide protons that indicate that the H helix is translocated (indicated by arrow and dotted ellipse). The H helix is also translocated in intermediate Ib, which contains more protected amides in the D and E helices, indicating that these helices are partly folded. After a few seconds, the final folded state forms, with all of the helices except F correctly folded and packed.

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