Molecular dynamics study of the conformational behavior of a representative elastin building block: Boc‐Gly‐Val‐Gly‐Gly‐Leu‐Ome

Lelj, Francesco; Tamburro, Antonio Mario; Villani, Vincenzo; Grimaldi, P.; Guantieri, Valeria

doi:10.1002/bip.360320206

Cited by 50 publications

(37 citation statements)

References 22 publications

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“…These were obtained from the trajectories analysis starting either from 50 or 110 ps on the basis of the above criteria. Although the torsions mean values differ at most of l.r, the corresponding rms significantly vary up to 41% of the 'soft' value as in the case of <h Significant variations are observed also for torsional correlation coefficients, in particular for 'If 1 '1'3 and '1' 3 'If 4 . Also the variations of interaction distances dij are large.…”

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confidence: 81%

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Conformational Modeling of Elastin Tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe by Molecular Dynamics Simulations with Improvements to the Thermalization Procedure

Villani

Tamburro²

1995

Journal of Biomolecular Structure and Dynamics

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Molecular Dynamics Simulations (MD) at Constant-Temperature or Constant-total Energy for the conformational Global-Minimum (GM) of elastin tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe have been performed. The thermalization problem concerning the initial state of Constant-Temperature MD has been solved developing two effective strategies. In the first one, the run starts from the room-temperature state reached by Molecular Dynamics Simulated Annealing (SA). In the second one, one starts from the annealed-state at low-temperature and performs a long constant-low-temperature run until the initial conformer is perfectly equilibrated. Then, the low-temperature equilibrated-state is used as initial state for MD at room-temperature. heuristic criteria on order to define the onset of steady-state have been established monitoring the hystories of collective parameters (e.g., the total energy, temperature, end-to-end distance, etc.) and their amplitude fluctuations. Moreover, the equilibrium between the system and the heat bath is verified analyzing the total linear momentum conservation by the time evolution of center mass velocity. The slow drift of total energy during Constant-total Energy MD has been corrected using a loose coupling between the system and the heat bath. Moreover, we have verified that the roto-translational motions do not affect significantly the properties of molecular vibrations. The librations of peptide unit inside the type II beta-turn [Gly1]C = 0 ... HN[Gly4], previously detected, were confirmed. Large -Gly-Gly- chain motions were identified and modeled as fluctuations occurring between the tetratepeptide GM and the saddle-point corresponding to the transition state of the conversion toward the extended-chain conformation. All these peptide motions could contribute to the elasticity mechanism of elastin.

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confidence: 81%

“…The model force field and the simulation software are the same used in our previous papers of this series (see references 3,5,6,8).…”

Section: Methodsmentioning

confidence: 99%

Conformational Modeling of Elastin Tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe by Molecular Dynamics Simulations with Improvements to the Thermalization Procedure

Villani

Tamburro²

1995

Journal of Biomolecular Structure and Dynamics

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“…2) along the chain. 43,44 Thus a regular array of b-turns (the Urry b-spiral) cannot be stable enough for these sequences, and the polypeptide chain is freely fluctuating (variable end-to-end distance), according to the classical theory of rubber elasticity.…”

Section: Elastinmentioning

confidence: 98%

Investigating by CD the molecular mechanism of elasticity of elastomeric proteins

2008

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Elastomeric proteins are widespread in the animal kingdom, and their main function is to confer elasticity and resilience to organs and tissues. Besides common functional properties, elastomeric proteins share a common sequence design. They are usually constituted by repetitive sequences with a high content of glycine residues. From a conformational point of view, all the elastomeric proteins since now analyzed show a dynamic equilibria between folded (mainly beta-turns) and extended (polyproline II and beta-strands) conformations that could be at the origin of the high entropy of the relaxed state. As a matter of fact, elastin, lamprin, abductin, as well as the PEVK domain of titin share the same conformational ensemble, thus pointing to a common molecular mechanism as the origin of elasticity. CD spectroscopy represents the proper spectroscopic technique to be used overall because of its particular sensitivity to the presence of PPII structure. Its use in the molecular studies of elastin, abductin, and lamprin as well as the recently analyzed protein resilin will be presented.

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“…[3] An important point to be emphasised is that, according to both NMR data and molecular dynamics simulations, the b turns are characterised by an extensive sliding, that is, they are interconverting with each other along the chain. This phenomenon, previously revealed by Tamburro and coworkers, [9,27] is considered as one of the possible sources of the entropy in the relaxed state of elastin. [28] Recently, analogously to the conclusions drawn for elastin and lamprin, an equilibrium comprising the PPII, b turn and unordered conformations has been suggested as a major structural feature for elastic segments of titin.…”

Section: Glagmentioning

confidence: 98%

Dissection of Human Tropoelastin: Solution Structure, Dynamics and Self‐Assembly of the Exon 5 Peptide

Bochicchio

Floquet

Pepe

et al. 2004

Chemistry A European J

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The elastic properties of elastin have essentially been discussed in terms of dominant entropic components, with questions still remaining about whether the basic mechanism is compatible with the classical theory of rubber elasticity. A better understanding of the structure-function relationships in terms of the protein's elastic properties remains an important goal in elastin science. Recently, we succeeded in the exon-by-exon synthesis of all polypeptide sequences encoded by the so-called hydrophobic exons and almost all of the cross-linking exons of human tropoelastin. Among these, the peptide encoded by exon 5 (PGGLAGAGLGA) has been extensively studied by classical spectroscopic methods, such as CD and NMR spectroscopy, and by molecular dynamics simulations. The results obtained clearly evidenced a large flexibility of the polypeptide chain, which oscillates between rather extended conformations, such as PPII, and folded ones, such as beta turns. At the supramolecular level, we obtained evidence by TEM that shows that the peptide encoded by exon 5 is able to self-assemble in fibrillar structures, a result indicating that the "information" for self-assembly is also contained within a small domain of tropoelastin.

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Molecular dynamics study of the conformational behavior of a representative elastin building block: Boc‐Gly‐Val‐Gly‐Gly‐Leu‐Ome

Cited by 50 publications

References 22 publications

Conformational Modeling of Elastin Tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe by Molecular Dynamics Simulations with Improvements to the Thermalization Procedure

Conformational Modeling of Elastin Tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe by Molecular Dynamics Simulations with Improvements to the Thermalization Procedure

Investigating by CD the molecular mechanism of elasticity of elastomeric proteins

Dissection of Human Tropoelastin: Solution Structure, Dynamics and Self‐Assembly of the Exon 5 Peptide

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