The role of loop closure propensity in the refolding of Rop protein probed by molecular dynamics simulations

Shukla, Rashmi Tambe; Baliga, Chetana; Sasidhar, Yellamraju U.

doi:10.1016/j.jmgm.2012.12.007

Cited by 5 publications

(14 citation statements)

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“…The loop region and the hydrophobic core have thereby attracted particular attention, as these regions are linked with the remarkable ability of Rop mutants to adopt altered topologies and properties (10)(11)(12)(13)(14)(15). Striking examples of loop variants include mutant Loopless Rop (LLR), in which an uninterrupted pattern of heptad repeats is established through a five-residue deletion in the loop.…”

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confidence: 99%

Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein

Amprazi

Kotsifaki

Providaki

et al. 2014

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

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The dimeric Repressor of Primer (Rop) protein, a widely used model system for the study of coiled-coil 4-α-helical bundles, is characterized by a remarkable structural plasticity. Loop region mutations lead to a wide range of topologies, folding states, and altered physicochemical properties. A protein-folding study of Rop and several loop variants has identified specific residues and sequences that are linked to the observed structural plasticity. Apart from the native state, native-like and molten-globule states have been identified; these states are sensitive to reducing agents due to the formation of nonnative disulfide bridges. Pro residues in the loop are critical for the establishment of new topologies and molten globule states; their effects, however, can be in part compensated by Gly residues. The extreme plasticity in the assembly of 4-α-helical bundles reflects the capacity of the Rop sequence to combine a specific set of hydrophobic residues into strikingly different hydrophobic cores. These cores include highly hydrated ones that are consistent with the formation of interchain, nonnative disulfide bridges and the establishment of molten globules. Potential applications of this structural plasticity are among others in the engineering of bio-inspired materials.recurrent tertiary motifs | core packing | disulfide bonds | dimensionless Kratky plot R ecurrent motifs of tertiary structure are convenient model systems for studying protein folding and potentially also for the design of bio-inspired materials. For protein design purposes, structural plasticity is an important, although poorly understood, parameter to be considered, as it is among the main reasons that the re-engineering of proteins toward novel materials is not yet satisfactorily manageable (1, 2).The present study focuses on the structural plasticity associated with the 4-α-helical bundle (4HB) motif. 4HBs consist of four amphipathic α-helices packed in a parallel or antiparallel fashion (3, 4). Their folding is largely determined by a repeating pattern of hydrophobic and hydrophilic residues, organized on the basis of seven-residue repeats (heptads) (5). Being the simplest tertiary motif, 4HBs have been subject to numerous proteinfolding studies; attempts have been made to exploit them as building blocks for bio-inspired materials (6).A paradigm of a highly regular 4HB is the RNA-binding ColE1 Repressor of Primer (Rop) protein (7-9), also referred to as RNA-one-modulator (ROM). Each monomer is an α-helical hairpin consisting of two antiparallel α-helices connected by a short loop. The sequence of Rop displays a heptad repeats pattern that is interrupted only in the loop region.Structural simplicity makes Rop an attractive model system for the study of the folding of 4HBs. The loop region and the hydrophobic core have thereby attracted particular attention, as these regions are linked with the remarkable ability of Rop mutants to adopt altered topologies and properties (10-15). Striking examples of loop variants include mutant Loopless Rop...

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confidence: 99%

Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein

Amprazi

Kotsifaki

Providaki

et al. 2014

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

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“…Basic structural simplicity makes Rop a very attractive model system for protein folding studies. The loop region has attracted particular attention because it is associated with the discontinuity of the heptads pattern, and is linked with the remarkable ability of several Rop mutants to adopt altered topologies and physicochemical properties including stability [ 10 , 18 , 19 , 33 , 34 , 35 ]. A striking example of loop variants includes the mutant RM6, in which a continuous pattern of heptad repeats is established through mutagenesis by the deletion of five loop residues.…”

Section: Introductionmentioning

confidence: 99%

Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments

Arnittali

Rissanou

Amprazi

et al. 2021

IJMS

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In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.

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“…We have been probing the role played by reverse turn/loop formation in protein folding through molecular dynamics simulations of peptide models. 19−21 Recently, by considering the peptide models of loop mutants of a four helix bundle protein, Rop, we have shown that there is a correlation between loop propensity 20 and experimental folding rates. 22 In this paper we will be focusing on the role played by the βturn region, 20 DPNL 23 , in the folding of Z34C, which is a small helix-turn-helix protein (α-helical hairpin/HTH motif).…”

Section: ■ Introductionmentioning

confidence: 99%

“…19−21 Recently, by considering the peptide models of loop mutants of a four helix bundle protein, Rop, we have shown that there is a correlation between loop propensity 20 and experimental folding rates. 22 In this paper we will be focusing on the role played by the βturn region, 20 DPNL 23 , in the folding of Z34C, which is a small helix-turn-helix protein (α-helical hairpin/HTH motif). The helix-turn-helix motif is a common denominator in many supersecondary structural elements.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Experimental studies involving infrared temperature-jump spectroscopy and circular dichroism have determined that the folding mechanism of the HTH motif from Z34C involves the turn region 20 DPNL 23 in the transition state of folding. 24 It is further suggested that the transition state contains native or native-like contacts and thus the formation of the β-turn paves the way for the folding of the α-helical hairpin.…”

Section: ■ Introductionmentioning

confidence: 99%

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Impact of Turn Propensity on the Folding Rates of Z34C Protein: Implications for the Folding of Helix-Turn-Helix Motif

Gupta

Sasidhar

2017

J. Phys. Chem. B

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The rate-limiting step for the folding of the helix-turn-helix (HTH) protein, Z34C, involves β-turn region DPNL. This reverse turn has been observed to be part of the transition state in the folding process for Z34C, influencing its folding rates. Molecular dynamics simulations were performed on this turn peptide and its two mutants, D20A and P21A, to study turn formation using GROMOS54A7 force field. We find that this region has a turn propensity of its own, and the highest turn propensity is observed for the wild-type, which correlates well with available experimental results. We also find that a slight unfavorable change in ΔG causes a drastic change in the folding rates of HTH motif and a mechanistic interpretation is given. Implications of these observations for the folding of the HTH protein Z34C are discussed.

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The role of loop closure propensity in the refolding of Rop protein probed by molecular dynamics simulations

Cited by 5 publications

References 55 publications

Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein

Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein

Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments

Impact of Turn Propensity on the Folding Rates of Z34C Protein: Implications for the Folding of Helix-Turn-Helix Motif

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