Cooperativity network of Trp‐cage miniproteins: probing salt‐bridges

Rovó, Petra; Farkas, Viktor; Hegyi, Orsolya; Szolomájer-Csikós, Orsolya; Tóth, Gábor; Perczel, András

doi:10.1002/psc.1377

Cited by 37 publications

(59 citation statements)

References 51 publications

(96 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…On the other hand, proton-proton NOEs between the side chain nuclei of Asp 9 and Arg 16– separated, on average, by approximately 4.5 Å in the NMR structure of the native state – cannot be detected. Despite its crucial role in stabilizing the globular fold of the native peptide [9], [20], [35], the denatured state hence seems to lack the Asp 9/Arg 16 salt bridge, and the results presented here seem to suggest that it is rather the aliphatic part of the arginine side chain found to be associated with Trp 6 in the 6 M urea-denatured state.…”

Section: Resultscontrasting

confidence: 51%

“…analysis of the structural properties of TC5b at varying denaturant concentrations and the subsequent transition state indispensable for the formation of a putatively populated folding intermediate [35], [70], the results presented here provide new insights into the structure and dynamic properties of the 6 M urea-unfolded state revealing significant non-random structure within this ensemble from which folding might commence. As such, we believe that the data help to bridge the gap between both the experimental work performed on ultrafast folding proteins and, on the other hand, molecular dynamics simulation studies.…”

Section: Resultsmentioning

confidence: 75%

See 1 more Smart Citation

Atomic-Level Structure Characterization of an Ultrafast Folding Mini-Protein Denatured State

et al. 2012

View full text Add to dashboard Cite

Atomic-level analyses of non-native protein ensembles constitute an important aspect of protein folding studies to reach a more complete understanding of how proteins attain their native form exhibiting biological activity. Previously, formation of hydrophobic clusters in the 6 M urea-denatured state of an ultrafast folding mini-protein known as TC5b from both photo-CIDNP NOE transfer studies and FCS measurements was observed. Here, we elucidate the structural properties of this mini-protein denatured in 6 M urea performing 15N NMR relaxation studies together with a thorough NOE analysis. Even though our results demonstrate that no elements of secondary structure persist in the denatured state, the heterogeneous distribution of R 2 rate constants together with observing pronounced heteronuclear NOEs along the peptide backbone reveals specific regions of urea-denatured TC5b exhibiting a high degree of structural rigidity more frequently observed for native proteins. The data are complemented with studies on two TC5b point mutants to verify the importance of hydrophobic interactions for fast folding. Our results corroborate earlier findings of a hydrophobic cluster present in urea-denatured TC5b comprising both native and non-native contacts underscoring their importance for ultra rapid folding. The data assist in finding ways of interpreting the effects of pre-existing native and/or non-native interactions on the ultrafast folding of proteins; a fact, which might have to be considered when defining the starting conditions for molecular dynamics simulation studies of protein folding.

show abstract

Section: Resultscontrasting

confidence: 51%

Section: Resultsmentioning

confidence: 75%

Atomic-Level Structure Characterization of an Ultrafast Folding Mini-Protein Denatured State

et al. 2012

View full text Add to dashboard Cite

show abstract

“…In addition, the abundant availability of the native states brings the observation of the existence of two substates in the native region. The molecular structures of two substates are in agreement with the previous computational 33,34 and experimental 34,35 studies. Moreover, three possible folding pathways are observed in the analyzing of C α -C α (helix) RMSD relationship, which indicates that various mechanisms might exist in the folding of trp-cage protein.…”

Section: Concluding Discussionsupporting

confidence: 89%

“…Between the two substates, the N-terminal helixes of the two structures are almost the same, and differences between the two are mainly caused by the C-terminal polyproline region. Our observation is consistent with the previous computational 33,34 and experimental 34,35 studies about the existence of these two substates.…”

Section: Small Protein Foldingsupporting

confidence: 93%

Parallel continuous simulated tempering and its applications in large-scale molecular simulations

Zang

Zhang

et al. 2014

The Journal of Chemical Physics

View full text Add to dashboard Cite

In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2-3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, LennardJones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.

show abstract

“…Monomer, native form of D9E and D9S mutants show helical structure, as reported previously. 26,29,30 All the phosphorylated mutant monomers proved to be disordered exhibiting spectra similar to that of D9E at 60 °C ( Fig. 2A and Fig.…”

Section: Monomer Structures From Nmr Chemical Shift Deviation (Csd)mentioning

confidence: 86%

Phosphorylation as Conformational Switch from the Native to Amyloid State: Trp-Cage as a Protein Aggregation Model

et al. 2015

Self Cite

View full text Add to dashboard Cite

The 20 residue long Trp-cage miniprotein is an excellent model both for computational and experimental studies of protein folding and stability. Recently, a great attention emerged to study disease-related protein misfolding, aggregation and amyloid formation, with the aim of revealing their structural and thermodynamic background. Trp-cage is sensitive to both environmental and structure-modifying effects, and aggregates with ease upon structure destabilization and thus, it is an ideal model of aggregation and amyloid formation. Here, we characterize the amyloid formation of several sequence modified and side-chain phosphorylated Trp-cage variants. We applied NMR, CD, FTIR spectroscopy, MD simulations, transmission electron microscopy in conjunction with thioflavin-T fluorescence measurements to reveal the structural consequences of side-chain phosphorylation. We demonstrate that the native fold is destabilized upon serine phosphorylation and the resultant highly dynamic structures form amyloid-like ordered aggregates with high intermolecular β-structure content. The only exception is the D9S(P) variant which follows an alternative aggregation process by forming thin fibrils, presenting a CD spectrum of PPII helix, and showing low ThT binding capability. We propose a complex aggregation model for these Trp-cage miniproteins. This model assumes an additional aggregated state, a collagen triple helical form which can precede amyloid formation. The phosphorylation of a single serine residue serves as a conformational switch, triggering aggregation, otherwise mediated by kinases in cell. We show that Trp-cage miniprotein is indeed a realistic model of larger globular systems of composite folding and aggregation landscapes and helps us to understand the fundamentals of deleterious protein aggregation and amyloid formation.3

show abstract

Cooperativity network of Trp‐cage miniproteins: probing salt‐bridges

Cited by 37 publications

References 51 publications

Atomic-Level Structure Characterization of an Ultrafast Folding Mini-Protein Denatured State

Atomic-Level Structure Characterization of an Ultrafast Folding Mini-Protein Denatured State

Parallel continuous simulated tempering and its applications in large-scale molecular simulations

Phosphorylation as Conformational Switch from the Native to Amyloid State: Trp-Cage as a Protein Aggregation Model

Contact Info

Product

Resources

About