The internal rotational barriers about NCα and CαC backbone bonds of polypeptides

Basharov, M. A.

doi:10.1007/s00249-011-0757-5

Cited by 5 publications

(5 citation statements)

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“…The observed activation energy of 33 kJ/mol for τ int may be interpreted as the roughness of the local energy landscape of intrachain interactions. This value might also be related to the peptide rotational barrier for the NC α bonds of about 66 kJ/mol and the C α C bond of about 25 kJ/mol . While the NC α bonds are assumed to be stiff, the C α C barrier fits reasonably well to our observation.…”

Section: Discussionsupporting

confidence: 81%

Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model

et al. 2021

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Disordered regions as found in intrinsically disordered proteins (IDP) or during protein folding define response time to stimuli and protein folding times. Neutron spin-echo spectroscopy is a powerful tool to directly access the collective motions of the unfolded chain to enlighten the physical origin of basic conformational relaxation. During the thermal unfolding of native ribonuclease A, we examine the structure and dynamics of the disordered state within a two-state transition model using polymer models, including internal friction, to describe the chain dynamics. The presence of four disulfide bonds alters the disordered configuration to a more compact configuration compared to a Gaussian chain that is defined by the additional links, as demonstrated by coarse-grained simulation. The dynamics of the disordered chain is described by Zimm dynamics with internal friction (ZIF) between neighboring amino acids. Relaxation times are dominated by mode-independent internal friction. Internal friction relaxation times show an Arrhenius-like behavior with an activation energy of 33 kJ/mol. The Zimm dynamics is dominated by internal friction and suggest that the characteristic motions correspond to overdamped elastic modes similar to the motions observed for folded proteins but within a pool of disordered configurations spanning the configurational space. For IDP, internal friction dominates while solvent friction and hydrodynamic interactions are smaller corrections.

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Section: Discussionsupporting

confidence: 81%

Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model

et al. 2021

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“…Usually, the torsional barrier parametrizations in classical force fields use a low number of Fourier terms to avoid an excessive computational cost, being the most common from one up to three terms. However, the modeling of more complex torsional profiles leads to the use of a larger number of Fourier terms, e.g., in the modeling of the torsional profile of biisothianaphthene molecule 25 or the calix [4]arene-substituted poly(thiophene) backbone. 6 Figure 2b shows the five-term Fourier fitting curve to B3LYP/ 6-311++G** torsional profile.…”

Section: Classical Model: Parameterization Of the Rotational Profilementioning

confidence: 99%

“…The correct description of this type of interaction in modern force fields (FFs) becomes important, as there is no specific parametrization for each case. In fact, critical torsions such as (φ – ψ) in proteins have been problematic and extensively studied, which has led to numerous reparametrizations and artifacts in the preponderance of secondary structures . Similarly, additional FF reparametrizations are needed in conjugated polymer simulations, where the potential energy curves around the torsional bonds connecting aromatic residues are not well described. , …”

Section: Introductionmentioning

confidence: 99%

Building a Torsional Potential between Thiophene Rings to Illustrate the Basics of Molecular Modeling

Torras

2022

J. Chem. Educ.

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Modeling an inter-ring torsional profile of a simple 2,2′-bithiophene molecule has been used to illustrate the main concepts associated with basic molecular modeling within an introductory course in a master’s degree on computational modeling. The methodology proposed in the activity has been used to guide and train the student along the classical and quantum model concepts visited along the main subject. The common thread that links the different concepts being learned is based on the deficiencies that usual force fields present in the right description of the torsional profiles. The students have learned how to obtain and implement the torsional profile of 2,2′-bithiophene to obtain the correct conformer population distribution and compare it to the distribution obtained using a predetermined classical force field. On the basis of the results obtained along the implementation of this activity and the student surveys, we conclude that this lab activity was successful as a complement to help students to understand the basic concepts of molecular modeling.

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“…The observed discrepancy between r Cu-H in residues 5 and 6 can be assigned to the difference between static DFT calculations and low rotation barriers of the side chains of 5 and 6 residues in real complexes. [37][38][39] A and B complexes have a similar internal hydrogen bond (HB) network. We found 5 HBs in complex A and 4 HBs in complex B (Table 4).…”

Section: Investigation Of Cu(ii) Binding By Viomycinmentioning

confidence: 99%

Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

et al. 2016

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Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidrug-resistant tuberculosis. In this paper we provide the characteristics of its acid base properties, coordination preferences towards the Cu(ii) ions, as well as the reactivity of the resulting complexes against plasmid DNA and HDV ribozyme. Careful coordination studies throughout the wide pH range allow for the characterisation of all the Cu(ii)-viomycin complex species. The assignment of proton chemical shifts was achieved by NMR experiments, while the DTF level of theory was applied to support molecular structures of the studied complexes. The experiments with the plasmid DNA reveal that at the physiological levels of hydrogen peroxide the Cu(ii)-viomycin complex is more aggressive against DNA than uncomplexed metal ions. Moreover, the degradation of DNA by viomycin can be carried out without the presence of transition metal ions. In the studies of antigenomic delta ribozyme catalytic activity, viomycin and its complex are shown to modulate the ribozyme functioning. The molecular modelling approach allows the indication of two different locations of viomycin binding sites to the ribozyme.

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The internal rotational barriers about NCα and CαC backbone bonds of polypeptides

Cited by 5 publications

References 31 publications

Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model

Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model

Building a Torsional Potential between Thiophene Rings to Illustrate the Basics of Molecular Modeling

Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

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