Molecular basis of thermal stability in truncated (2/2) hemoglobins

Bustamante, Juan Pablo; Bonamore, Alessandra; Nadra, Alejandro D.; Sciamanna, Natascia; Boffi, Alberto; Estrin, Darı́o A.; Boechi, Leonardo

doi:10.1016/j.bbagen.2014.03.018

Cited by 9 publications

(6 citation statements)

References 44 publications

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“…Introduction of proline residues increases protein stability and has been successfully reported in industrial enzymes. In particular, proline residues at specific sites, such as β-turns or loop regions, are more effective for protein thermostability (Tian et al, 2010;Bustamante et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

Residues 315 and 369 in HN Protein Contribute to the Thermostability of Newcastle Disease Virus

Ruan

Zhang

et al. 2020

Front. Microbiol.

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Thermostable Newcastle disease virus (NDV) vaccines have been widely used in areas where a "cold-chain" is not reliable. However, the molecular mechanism of NDV thermostability remains poorly understood. In this work, we constructed chimeric viruses by exchanging viral fusion (F) and/or hemagglutinin-neuraminidase (HN) genes between the heat-resistant strain HR09 and thermolabile strain La Sota utilizing a reverse genetic system. The results showed that only chimeras with HN derived from the thermostable virus exhibited a thermostable phenotype at 56 • C. The hemagglutinin (HA) and neuraminidase (NA) activities of chimeras with HN derived from the HR09 strain were more thermostable than those containing HN from the La Sota strain. Then, we used molecular dynamics simulation at different temperatures (310 K and 330 K) to measure the HN protein of the La Sota strain. The conformation of an amino acid region (residues 315-375) was observed to fluctuate. Sequence alignment of the HN protein revealed that residues 315, 329, and 369 in the La Sota strain and thermostable strains differed. Whether the three amino acid substitutions affected viral thermostability was investigated. Three mutant viruses based on the thermolabile strain were generated by substituting one, two or three amino acids at positions 315, 369, and 329 in the HN protein. In comparison with the parental virus, the mutant viruses containing mutations S315P and I369V possessed higher thermostablity and HA titers, NA and fusion activities. Taken together, these data indicate that the HN gene of NDV is a major determinant of thermostability, and residues 315 and 369 have important effects on viral thermostability.

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Section: Discussionmentioning

confidence: 99%

Residues 315 and 369 in HN Protein Contribute to the Thermostability of Newcastle Disease Virus

Ruan

Zhang

et al. 2020

Front. Microbiol.

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“…In order to obtain a reliable conformational analysis of a biological system in a molecular dynamics simulation, an accurate force field is essential. Different force field parameters have been generated in order to reproduce X-ray structures, interaction energies, and spectroscopic information on heme model systems. , In this work, we used a force field designed in our group that has been shown to provide reliable results in representing the structure and dynamics of the active sites of heme proteins and also as a first step for generating initial configurations for more sophisticated QM/MM calculations. − …”

Section: Theoretical Calculationsmentioning

confidence: 99%

In Silico Insight into the Reductive Nitrosylation of Ferric Hemeproteins

2020

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A combination of in silico methods was used to extend the experimental description of the reductive nitrosylation mechanism in ferric hemeproteins with the molecular details of the role of surrounding amino acids. The computational strategy consisted in the estimation of potential energy profiles for the transition process associated with the interactions of the coordinated N(NO) moiety with O(H 2 O) or O(OH − ) as nucleophiles, and with distal amino acids as proton acceptors or affecting the stability of transition states. We inspected the reductive nitrosylation in three representative hemeproteins -sperm whale metmyoglobin, α subunit of human methemoglobin and nitrophorin 4 of Rhodnius prolixus. For each case, classical molecular dynamics simulations were performed in order to obtain relevant reactive conformations, and a potential energy profile for the reactive step was obtained using adiabatic mapping or nudged elastic band approaches at the QM/MM level. Specifically, we report the role of a charged Arg45 of myoglobin in destabilizing the transition state when H 2 O acts as nucleophile, differently to the neutral Pro43 of the hemoglobin subunit. The case of the nitrophorin is unique in that the access of the required water molecules is scarce, thus, preventing the reaction.

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“…23 Indeed, a more recent work that compares the thermal stabilities of truncated hemoglobins from mesophilic and thermophilic organisms indicates that proteins with higher flexibility display higher thermal stability. 24 Thus, it is not straightforward to predict a priori the effect of protein flexibility on thermal stability.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Thus, a larger number of contacts in the native state, which is typically associated with a greater rigidity of the protein structure, will favor the enthalpic contribution and benefit high thermal stability. − On the other hand, in regard to the entropic contribution to the thermal stability, a larger conformational entropy in the folded state, which is typically associated with higher flexibility of the protein structure, will also benefit thermal stability . Indeed, a more recent work that compares the thermal stabilities of truncated hemoglobins from mesophilic and thermophilic organisms indicates that proteins with higher flexibility display higher thermal stability . Thus, it is not straightforward to predict a priori the effect of protein flexibility on thermal stability.…”

Section: Introductionmentioning

confidence: 99%

Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations

Plana

Nadra

Estrin

et al. 2018

J. Chem. Inf. Model.

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Proteins are sensitive to temperature, and abrupt changes in the normal temperature conditions can have a profound impact on both structure and function, leading to protein unfolding. However, the adaptation of certain organisms to extreme conditions raises questions about the structural features that permit the structure and function of proteins to be preserved under these adverse conditions. To gain insight into the molecular basis of protein thermostability in the globin family, we have examined three representative examples: human neuroglobin, horse heart myoglobin, and Drosophila hemoglobin, which differ in their melting temperatures and coordination states of the heme iron in the absence of external ligands. In order to elucidate the possible mechanisms that govern the thermostability of these proteins, microsecond-scale classical molecular dynamics simulations were performed at different temperatures. Structural fluctuations and essential dynamics were analyzed, indicating that the flexibility of the CD region, which includes the two short C and D helixes and the connecting CD loop, is directly related to the thermostability. We observed that a larger inherent flexibility of the protein produces higher thermostability, probably concentrating the thermal fluctuations observed at high temperature in flexible regions, preventing unfolding. Globally, the results of this work improve our understanding of thermostability in the globin family.

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Molecular basis of thermal stability in truncated (2/2) hemoglobins

Cited by 9 publications

References 44 publications

Residues 315 and 369 in HN Protein Contribute to the Thermostability of Newcastle Disease Virus

Residues 315 and 369 in HN Protein Contribute to the Thermostability of Newcastle Disease Virus

In Silico Insight into the Reductive Nitrosylation of Ferric Hemeproteins

Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations

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