Exploiting the downhill folding regime via experiment

Muñoz, Víctor; Sadqi, Mourad; Naganathan, Athi N.; Sancho, David De

doi:10.2976/1.2988030

Cited by 25 publications

(28 citation statements)

References 57 publications

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“…However, whether this difference in native structures of Naf-BBL and QNND-BBL in protein data bank ͑PDB͒ files is actually responsible for the different folding behaviors is still questionable, because the nuclear overhauser effect ͑NOE͒ maps obtained from NMR experiments for these two variants are similar, indicating an almost identical interaction network of these two variants. 12 Here, the different degrees of folding cooperativity of Naf-BBL and QNND-BBL in our simulation are clearly originated from the different native structures in their PDB files. The sensitivity of folding behavior to the change in tertiary native contacts indicates the importance of the tertiary native structure in determining the folding cooperativity.…”

Section: A Weak Cooperative Folding Of Naf-bblmentioning

confidence: 71%

“…6,7 However, there are also controversial issues in whether the folding of BBL is globally downhill or not. In several previously experimental and theoretical researches, 8-10 the QNND-BBL, which has an extended N-terminal tail comparing to Naf-BBL, has been reported to have different folding behavior compared with Naf-BBL, but the methods used to interpret the experimental data and the origin of the different folding behaviors of the two variants of BBL in simulations are under debate, 11,12 and there are accumulating experimental evidences suggesting that the two variants should have similar folding behaviors. 11,[13][14][15] Therefore, the problem of downhill folding is still an ongoing research issue, but it is unquestionable that the folding cooperativity of BBL is substantially smaller than those of typical two-state proteins.…”

Section: Introductioinmentioning

confidence: 99%

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Understanding protein folding cooperativity based on topological consideration

Liu

et al. 2009

The Journal of Chemical Physics

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The folding cooperativity is an important issue of protein folding dynamics. Since the native topology plays a significant role in determining the folding behavior of proteins, we believe that it also has close relationship with the folding cooperativity. In the present work, we perform simulations on proteins Naf-BBL, QNND-BBL, CI2, and SH3 with the Gō model and compare their different folding behaviors. By analyzing the weak cooperative folding of protein Naf-BBL in detail, we found that the folding of Naf-BBL shows relatively weak thermodynamic coupling between residues, and such weak coupling is found mainly between the nonlocal native contacts. This finding complements our understandings on the source of barrierless folding of Naf-BBL and promotes us to analyze the topological origins of the poor thermodynamic coupling of Naf-BBL. Then, we further extend our analysis to other two-state and multistate proteins. Based on the considerations of the thermodynamic coupling and kinetic coupling, we conclude that the fraction of scattered native contacts, the difference in loop entropy of contacts, and the long range relative contact order are the major topological factors that influence the folding cooperativity. The combination of these three tertiary structural features shows significant correlations with the folding types of proteins. Moreover, we also discuss the topological factors related to downhill folding. Finally, the generic role of tertiary structure in determining the folding cooperativity is summarized.

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Section: A Weak Cooperative Folding Of Naf-bblmentioning

confidence: 71%

Section: Introductioinmentioning

confidence: 99%

Understanding protein folding cooperativity based on topological consideration

Liu

et al. 2009

The Journal of Chemical Physics

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“…[116][117][118][119][120][121] This approach is simple and recapitulates existing experimental procedures to modify folding barriers through site-directed mutations. 43,52,58,115,[122][123][124][125][126][127] DNA recognition of EngHD is a complex process involving standard 3D diffusion, non-specific binding through electrostatic interactions, 1D diffusive search along the DNA length via various types of modes, and lock into the target site. Our simulations on a CGSBM reproduce all these processes thus permitting us to dissect how each of them is affected by the conformational properties of EngHD.…”

Section: Discussionmentioning

confidence: 99%

Roles of conformational disorder and downhill folding in modulating protein–DNA recognition

Chu

Muñoz

2017

Phys. Chem. Chem. Phys.

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Transcription factors are thought to efficiently search for their target DNA site via a combination of conventional 3D diffusion and 1D diffusion along the DNA molecule mediated by non-specific electrostatic interactions. This process requires the DNA-binding protein to quickly exchange between a search competent and a target recognition mode, but little is known as to how these two binding modes are encoded in the conformational properties of the protein. Here, we investigate this issue on the engrailed homeodomain (EngHD), a DNA-binding domain that folds ultrafast and exhibits a complex conformational behavior consistent with the downhill folding scenario. We explore the interplay between folding and DNA recognition using a coarse-grained computational model that allows us to manipulate the folding properties of the protein and monitor its non-specific and specific binding to DNA. We find that conformational disorder increases the search efficiency of EngHD by promoting a fast gliding search mode in addition to sliding. When gliding, EngHD remains loosely bound to DNA moving linearly along its length. A partially disordered EngHD also binds more dynamically to the target site, reducing the half-life of the specific complex via a spring-loaded mechanism. These findings apply to all conditions leading to partial disorder. However, we also find that at physiologically relevant temperatures EngHD is well folded and can only obtain the conformational flexibility required to accelerate 1D diffusion when it folds/unfolds within the downhill scenario (crossing a marginal free energy barrier). In addition, the conformational flexibility of native downhill EngHD enables its fast reconfiguration to lock into the specific binding site upon arrival, thereby affording finer control of the on- and off-rates of the specific complex. Our results provide key mechanistic insights into how DNA-binding domains optimize specific DNA recognition through the control of their conformational dynamics and folding mechanism.

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“…In this analysis the thermal unfolding behavior of hundreds of individual atoms in the protein are monitored by NMR leading to a map of the folding interaction network of the protein [8]. However, before performing such analysis it is important to revisit the structural characterization of native gpW by NMR.…”

Section: Introductionmentioning

confidence: 99%

Revisiting the NMR Structure of the Ultrafast Downhill Folding Protein gpW from Bacteriophage λ

et al. 2011

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GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.

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Exploiting the downhill folding regime via experiment

Cited by 25 publications

References 57 publications

Understanding protein folding cooperativity based on topological consideration

Understanding protein folding cooperativity based on topological consideration

Roles of conformational disorder and downhill folding in modulating protein–DNA recognition

Revisiting the NMR Structure of the Ultrafast Downhill Folding Protein gpW from Bacteriophage λ

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