Probing the Interactions between the Folding Elements Early in the Folding of Escherichia coli Dihydrofolate Reductase by Systematic Sequence Perturbation Analysis

Arai, Munehito; Iwakura, Masahiro

doi:10.1016/j.jmb.2005.01.033

Cited by 27 publications

(50 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…At the characteristic times of t = τ A , τ B , and 3:0 × 10 6 t 0 , the distributions of positions of MC trajectories on the 2D space of ðM DLD ; M ABD Þ are shown in Fig.5 B-D. By comparing these results with the free-energy surface in Fig. 4A, no population of the simulated trajectories can be found that shifted toward I α , and the simulated DHFR folding follows a single sequential pathway of Path ABD , which is also consistent with experimental observations (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29). At the later phase of folding, the internal friction should begin to increase the timescale for the folding process (30)(31)(32).…”

Section: Resultssupporting

confidence: 82%

“…Although this simulated intermediate was interpreted as I HF (34), the DLD of the simulated intermediate was poorly structured, which was more similar to I 6 than to I HF or I 5 in which the structure of DLD is reasonably formed (19). Because experimental data for I 6 and I 5 became available (19,21,22) after this MD result was reported, we revisit the problem of the DHFR folding intermediates in this paper. To highlight the relationship between the topology of the native conformation and the folding pathway, we develop a simple theoretical model as an extension of the structure-based model first developed by Wako and Saito (35,36) that was systematically applied to proteins by Muñoz and Eaton (18).…”

Section: Significancementioning

confidence: 99%

“…Because DLD does not include a single contiguous region of the chain, but rather includes separate N-and C-terminal parts, the structural ordering of DLD can be correlated with the structural ordering of ABD. As a model protein, DHFR has been intensively investigated (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29), which has resulted in a picture that DHFR folds along the following pathway:…”

mentioning

confidence: 99%

“…I 6 appeared in τ 7 < 35 μs after folding was initiated from the unfolded state (U). During τ 6 ∼ 550 μs, further structural development was observed both in ABD and in DLD (19), which led to I 5 in which the secondary structures were reasonably formed (20)(21)(22) and two subsets of hydrogen-bonding networks were formed in ABD and DLD (23).…”

mentioning

confidence: 99%

See 3 more Smart Citations

Folding pathway of a multidomain protein depends on its topology of domain connectivity

Inanami

Terada

Sasai

2014

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

How do the folding mechanisms of multidomain proteins depend on protein topology? We addressed this question by developing an Ising-like structure-based model and applying it for the analysis of free-energy landscapes and folding kinetics of an example protein, Escherichia coli dihydrofolate reductase (DHFR). DHFR has two domains, one comprising discontinuous N-and C-terminal parts and the other comprising a continuous middle part of the chain. The simulated folding pathway of DHFR is a sequential process during which the continuous domain folds first, followed by the discontinuous domain, thereby avoiding the rapid decrease in conformation entropy caused by the association of the N-and C-terminal parts during the early phase of folding. Our simulated results consistently explain the observed experimental data on folding kinetics and predict an off-pathway structural fluctuation at equilibrium. For a circular permutant for which the topological complexity of wild-type DHFR is resolved, the balance between energy and entropy is modulated, resulting in the coexistence of the two folding pathways. This coexistence of pathways should account for the experimentally observed complex folding behavior of the circular permutant.folding intermediates | internal friction | eWSME model

show abstract

Section: Resultssupporting

confidence: 82%

Section: Significancementioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Folding pathway of a multidomain protein depends on its topology of domain connectivity

Inanami

Terada

Sasai

2014

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Circular permutation of a protein consists of connecting the native N-and C-termini covalently with a peptide linker and cleaving the peptide backbone at another specific site. Iwakura et al have performed systematic circular permutation of the entire DHFR protein to investigate essential folding elements [5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Ligand Binding and Circular Permutation modify Residue Interaction Network in DHFR

Hu¹,

Bowen²,

Southerland³

et al. 2005

PLoS Comput Biol

View full text Add to dashboard Cite

Residue interaction networks and loop motions are important for catalysis in dihydrofolate reductase (DHFR). Here, we investigate the effects of ligand binding and chain connectivity on network communication in DHFR. We carry out systematic network analysis and molecular dynamics simulations of the native DHFR and 19 of its circularly permuted variants by breaking the chain connections in ten folding element regions and in nine nonfolding element regions as observed by experiment. Our studies suggest that chain cleavage in folding element areas may deactivate DHFR due to large perturbations in the network properties near the active site. The protein active site is near or coincides with residues through which the shortest paths in the residue interaction network tend to go. Further, our network analysis reveals that ligand binding has ''network-bridging effects'' on the DHFR structure. Our results suggest that ligand binding leads to a modification, with most of the interaction networks now passing through the cofactor, shortening the average shortest path. Ligand binding at the active site has profound effects on the network centrality, especially the closeness.

show abstract

Mapping the interactions of adenoviral E1A proteins with the p160 nuclear receptor coactivator binding domain of CBP

et al. 2016

Self Cite

View full text Add to dashboard Cite

Many viruses deregulate the cell and force transcription of viral genes by competing with cellular proteins for binding to the transcriptional co-activators CREB-binding protein (CBP) and p300. Through its interactions with CBP/p300 and the retinoblastoma protein, the adenovirus (AdV) early region 1A (E1A) oncoprotein hijacks the cell cycle and, in rodents, transforms the cell; the mechanistic and structural basis for these effects remain unclear. In this study we compare the affinity of protein constructs from the E1A proteins from two adenovirus serotypes, non-oncogenic AdV5 and highly oncogenic AdV12, for binding to the nuclear receptor coactivator binding domain (NCBD) of CBP. NMR spectra show that the E1A constructs from both serotypes are intrinsically disordered in the free state and that each contains three homologous binding sites for the NCBD, one in the N-terminal region and two within conserved region 1 (CR1) of E1A. The binding sites in CR1 correspond to the motifs that bind the retinoblastoma protein and the TAZ2 domain of CBP/ p300. The E1A and NCBD peptides fold synergistically upon complex formation. Binding affinities determined from NMR titrations show that, although the overall affinities for AdV5 and AdV12 E1A are comparable, there are significant differences between the two E1A serotypes in the relative strength with which their constituent interaction motifs bind to the NCBD. The individual E1A interaction motifs were unable to compete effectively with p53 for binding to the NCBD and both the N-terminal region and CR1 region of E1A are required for efficient competition with p53.

show abstract

Probing the Interactions between the Folding Elements Early in the Folding of Escherichia coli Dihydrofolate Reductase by Systematic Sequence Perturbation Analysis

Cited by 27 publications

References 36 publications

Folding pathway of a multidomain protein depends on its topology of domain connectivity

Folding pathway of a multidomain protein depends on its topology of domain connectivity

Ligand Binding and Circular Permutation modify Residue Interaction Network in DHFR

Mapping the interactions of adenoviral E1A proteins with the p160 nuclear receptor coactivator binding domain of CBP

Contact Info

Product

Resources

About