High-resolution solution NMR structure of the Z domain of staphylococcal protein A

By using local (free-energy profiles along the amino acid sequence and 13 C α chemical shifts) and global (principal component) analyses to examine the molecular dynamics of protein-folding trajectories, generated with the coarse-grained united-residue force field, for the B domain of staphylococcal protein A, we are able to (i) provide the main reason for formation of the mirror-image conformation of this protein, namely, a slow formation of the second loop and part of the third helix (Asp29-Asn35), caused by the presence of multiple local conformational states in this portion of the protein; (ii) show that formation of the mirror-image topology is a subtle effect resulting from local interactions; (iii) provide a mechanism for how protein A overcomes the barrier between the metastable mirror-image state and the native state; and (iv) offer a plausible reason to explain why protein A does not remain in the metastable mirror-image state even though the mirror-image and native conformations are at least energetically compatible.misfolding | symmetrical proteins T o perform their functions in living organisms, most proteins must fold from unfolded polypeptides into their functional, unique 3D structures. Understanding protein-folding mechanisms is crucial because misfolded proteins can cause many diseases, including neurodegenerative diseases (1) such as Alzheimer's, Parkinson, and Huntington diseases. From theoretical and conceptual points of view, it has been suggested that a native protein exists in a thermodynamically stable state with its surroundings (2) and that a study of free-energy landscapes (FELs) holds the key to understanding how proteins fold and function (3, 4).The native structures of some proteins contain a high degree of symmetry that, in addition to the native structure, allows the existence of another, energetically very close to the native conformation, a native-like "mirror-image" structure. One of the representatives of such symmetrical proteins is the 10-to 55-residue fragment of the B domain of staphylococcal protein A [Protein Data Bank (PDB) ID: 1BDD, a three-α-helix bundle] (5). Protein A has been the subject of extensive theoretical (6-18) and experimental (19-23) studies because of its small size, fast folding kinetics, and biological importance. However, the mirror-image topology has never been a subject for discussion except for the earlier work by Olszewski et al. (7) and recent work by Noel et al. (24). The reason for this might be that it has never been detected experimentally and it was observed only in some theoretical studies (7-9, 12, 13, 15, 17, 18, 24) with different force fields. It is of interest to determine how realistic the mirror-image conformation is. Is it an artifact of the simulations or is it a conformation difficult to observe experimentally? Noel et al. (24) showed that the native and mirror-image structures have a similar enthalpic stability and are thermodynamically competitive and that the mirror image can be considered not just a computational annoyance...

mentioning

confidence: 72%

“…S6 show the bar corresponding to residue Gly21 highlighted in yellow, i.e., indicating that the observed 13 C α chemical shift value is missing. Overall, because the B and Z domains exhibit identical binding affinity (33), the use of the observed information from the Z rather than the B domain of protein A is reasonable.…”

mentioning

confidence: 98%

Accounting for a mirror-image conformation as a subtle effect in protein folding

Kachlishvili

Maisuradze

Martin

et al. 2014

“…The placement of the ring is supported by NOEs observed in the solution structure on another SpA domain between F5 and nearby residues [BioMagResBank (BMRB) accession no. 4023 (30)], depicted as dashes. However, in the complex structure, F5 flips outward to accommodate F c I253, which makes van der Waals interactions with the same pocket.…”

Section: Spa Contains An Important Molecular-recognition Pocket For Fmentioning

confidence: 99%

Suppression of conformational heterogeneity at a protein–protein interface

Deis

Wang

et al. 2015

Staphylococcal protein A (SpA) is an important virulence factor from Staphylococcus aureus responsible for the bacterium’s evasion of the host immune system. SpA includes five small three-helix–bundle domains that can each bind with high affinity to many host proteins such as antibodies. The interaction between a SpA domain and the Fc fragment of IgG was partially elucidated previously in the crystal structure 1FC2. Although informative, the previous structure was not properly folded and left many substantial questions unanswered, such as a detailed description of the tertiary structure of SpA domains in complex with Fc and the structural changes that take place upon binding. Here we report the 2.3-Å structure of a fully folded SpA domain in complex with Fc. Our structure indicates that there are extensive structural rearrangements necessary for binding Fc, including a general reduction in SpA conformational heterogeneity, freezing out of polyrotameric interfacial residues, and displacement of a SpA side chain by an Fc side chain in a molecular-recognition pocket. Such a loss of conformational heterogeneity upon formation of the protein–protein interface may occur when SpA binds its multiple binding partners. Suppression of conformational heterogeneity may be an important structural paradigm in functionally plastic proteins.

“…Despite its measured high stability as a fragment (32), Deisenhofer's early x-ray structure failed to reveal electron density for helix H3 when the domain was bound to its target immunoglobulin (33). NMR of the isolated domain shows helix H3 as intact, but NMR also reveals modest differences in the packing of H1 and H2 in the homologous Z domain of protein A (34,35). These can be taken to be signs of frustration in the domain: there is a modest inconsistency of energetic biases for secondary and tertiary structure.…”

Section: Devilish Detailsmentioning

confidence: 99%

Latest folding game results: Protein A barely frustrates computationalists

Wolynes

2004

T he dark mystery of protein folding has been greatly illuminated by the last decade's work. This enlightenment has come from the simultaneous flowering of new theoretical approaches (1-3), powerful computational studies (4,5), and a fresh wave of experiments using protein engineering (6) and ultrafast kinetics (7,8). How a disordered chain molecule finds its organized, folded state is no longer a paradox, but a scientific problem requiring a close comparison of theories, computation and experiments. A beautiful experimental study of the mechanism of folding of the B domain of streptococcal protein A appears in this issue of PNAS (9). This study joins such landmarks as the elucidation of the folding mechanism of CI2 and barnase by the same group (10). So what's the news? The excitement comes because this protein has been the poster child of computational folders. It is attractive to computationalists because of its small size, 60 residues, at the extreme limit exhibiting cooperative protein-like thermodynamics. The protein also folds fast, so computer studies have the best chance of success. Numerous simulations were carried out (11-23) without extensive laboratory kinetic studies at the residue level to influence the work. It is thus interesting to see how well the computationalists have been able to predict the folding mechanism without much biasing data. Sato et al. (9) liken the comparison of simulations with their kinetic experiment to the biennial exercise Critical Assessment of Structure Prediction (CASP) (24). They, like most participants in CASP, refer to it as a competition, although the organizers decry that appellation. As the leader of a participating group, I can testify to CASP's painfulness, but, despite its undignified similarity to a sporting event, good science comes from CASP. Likewise, the present results do indeed provoke serious thought.When compared with the old view of a single obligate folding pathway (25), the computational studies are in remarkable agreement with each other and with experiment. All these studies show a diffuse folding mechanism in which a fairly diverse ensemble of structures is guided to the native structure by trading stabilization free energy for configurational entropy (1). The energy landscape resembles a funnel in which more native-like structures are stabilized over kinetic traps that could arise from conflicting energetic signals (''frustration''). In a funnel landscape, although trapping is not a problem, a kinetic bottleneck arises because stabilization energy and entropy do not smoothly compensate each other as the protein descends in the funnel. The ensemble of structures at the bottleneck, called the transition state ensemble (TSE), is probed by examining the effect of changing individual amino acids on folding rates. In a funnel-like landscape, these changes can be converted to values that measure how much more structures in the TSE resemble the native structure or the denatured ensemble. If ϭ 1 for a given residue, in the TSE that residue will be in a ...