Effects of core-packing on the structure, function, and mechanics of a four-helix-bundle protein ROP

Ceruso, Marc A.; Grottesi, Alessandro; Nola, Alfredo Di

doi:10.1002/(sici)1097-0134(19990901)36:4<436::aid-prot7>3.0.co;2-l

Cited by 13 publications

(16 citation statements)

References 49 publications

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“…These data show that the dynamic properties of each subunit are regulated by their b-sheet topology rather than by the hinge peptide regions. This result is in line with previous investigations carried out on topologically similar proteins (Ceruso et al, 1999b;Keskin et al, 2000;Merlino et al, 2003).…”

Section: Discussionsupporting

confidence: 93%

“…This finding indicates that the b-sheet displays a breathing motion in both subunits. The comparison of the motions between the two N-Dimer structural units carried out by using the root mean-square inner product (Amadei et al, 1999;Ceruso et al, 1999bCeruso et al, , 2003Merlino et al, 2003) (RMSIP, see Methods for details) between the first 10 eigenvectors derived from the diagonalization of the covariance matrices (Table 1), reveals that they exhibit the same dynamic behavior. The high value of RMSIP indicates that the essential subspace spanned by the first 10 eigenvectors of the two N-Dimer structural units is largely overlapped (Table 1).…”

Section: C-interface Motions: Active Site Flexibilitymentioning

confidence: 99%

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Dynamic Properties of the N-Terminal Swapped Dimer of Ribonuclease A

Merlino

Vitagliano

Ceruso

et al. 2004

Biophysical Journal

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Bovine pancreatic ribonuclease (RNase A) forms two 3-dimensional domain-swapped dimers with different quaternary structures. One dimer is characterized by the swapping of the C-terminal region (C-Dimer) and presents a rather loose structure. The other dimer (N-Dimer) exhibits a very compact structure with exchange of the N-terminal helix. Here we report the results of a molecular dynamics/essential dynamics (MD/ED) study carried out on the N-Dimer. This investigation, which represents the first MD/ED analysis on a three-dimensional domain-swapped enzyme, provides information on the dynamic properties of the active site residues as well as on the global motions of the dimer subunits. In particular, the analysis of the flexibility of the active site residues agrees well with recent crystallographic and site-directed mutagenesis studies on monomeric RNase A, thus indicating that domain swapping does not affect the dynamics of the active sites. A slight but significant rearrangement of N-Dimer quaternary structure, favored by the formation of additional hydrogen bonds at subunit interface, has been observed during the MD simulation. The analysis of collective movements reveals that each subunit of the dimer retains the functional breathing motion observed for RNase A. Interestingly, the breathing motion of the two subunits is dynamically coupled, as they open and close in phase. These correlated motions indicate the presence of active site intercommunications in this dimer. On these bases, we propose a speculative mechanism that may explain negative cooperativity in systems preserving structural symmetry during the allosteric transitions.

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Section: Discussionsupporting

confidence: 93%

Section: C-interface Motions: Active Site Flexibilitymentioning

confidence: 99%

Dynamic Properties of the N-Terminal Swapped Dimer of Ribonuclease A

Merlino

Vitagliano

Ceruso

et al. 2004

Biophysical Journal

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“…We calculated the root‐mean‐square inner product RMSIP (see Materials and Methods) between the first 10 eigenvectors of each simulation. It has been reported48, 49 that this number accounts for the (dis)similarity of the essential motions. For reference values, we have divided each trajectory in two halves and have calculated the inner product between the first 10 essential eigenvectors of each half.…”

Section: Resultsmentioning

confidence: 91%

Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin

et al. 2002

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In recent years, increased interest in the origin of protein thermal stability has gained attention both for its possible role in understanding the forces governing the folding of a protein and for the design of new highly stable engineered biocatalysts. To study the origin of thermostability, we have performed molecular dynamics simulations of two rubredoxins, from the mesophile Clostridium pasteurianum and from the hyperthermophile Pyrococcus furiosus. The simulations were carried out at two temperatures, 300 and 373 K, for each molecule. The length of the simulations was within the range of 6-7.2 ns. The rubredoxin from the hyperthermophilic organism was more flexible than its mesophilic counterpart at both temperatures; however, the overall flexibility of both molecules at their optimal growth temperature was the same, despite 59% sequence homology. The conformational space sampled by both molecules was larger at 300 K than at 373 K. The essential dynamics analysis showed that the principal overall motions of the two molecules are significantly different. On the contrary, each molecule showed similar directions of motion at both temperatures.

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“…This technique is a powerful tool for investigating the structural and dynamic behavior of biological macromolecules 15, 16. MD simulations have been frequently used to study the effect of single point mutations17, 18 as well as the stability of protein fragments 19. A number of computational studies have also started addressing features of protein thermal stability 20–31.…”

Section: Introductionmentioning

confidence: 99%

Structural and dynamic effects of α‐Helix deletion in Sso7d: Implications for protein thermal stability

2004

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Sso7d is a 62-residue protein from the hyperthemophilic archaeon Sulfolobus solfataricus with a denaturation temperature close to 100 degrees C around neutral pH. An engineered form of Sso7d truncated at leucine 54 (L54Delta) is significantly less stable, with a denaturation temperature of 53 degrees C. Molecular dynamics (MD) studies of Sso7d and its truncated form at two different temperatures have been performed. The results of the MD simulations at 300 K indicate that: (1) the flexibility of Sso7d chain at 300 K agrees with that detected from X-ray and NMR structural studies; (2) L54Delta remains stable in the native folded conformation and possesses an overall dynamic behavior similar to that of the parent protein. MD simulations performed at 500 K, 10 ns long, indicate that, while Sso7d is in-silico resistant to high temperature, the truncated variant partially unfolds, revealing the early phases of the thermal unfolding pathway of the protein. Analysis of the trajectories of L54Delta suggests that the unzipping of the N-terminal and C-terminal beta-strands should be the first event of the unfolding pathway, and points out the regions more resistant to thermal unfolding. These findings allow one to understand the role played by specific interactions connecting the two ends of the chain for the high thermal stability of Sso7d, and support recent hypotheses on its folding mechanism emerged from site-directed mutagenesis studies.

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Effects of core-packing on the structure, function, and mechanics of a four-helix-bundle protein ROP

Cited by 13 publications

References 49 publications

Dynamic Properties of the N-Terminal Swapped Dimer of Ribonuclease A

Dynamic Properties of the N-Terminal Swapped Dimer of Ribonuclease A

Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin

Structural and dynamic effects of α‐Helix deletion in Sso7d: Implications for protein thermal stability

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