On the role of water in the protein activity

Degrève, Léo; Brancaleoni, G.H.; Fuzo, Carlos Alessandro; Lourenzoni, Marcos Roberto; Mazzé, Fernanda Marur; Namba, Adriana M.; Vieira, Davi Serradella

doi:10.1590/s0103-97332004000100014

Cited by 10 publications

(5 citation statements)

References 52 publications

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“…The aim of this paper is to identify how the membrane hydrophobic region helps to conserve the HNP dimer stability, identifying in this way the main factors that provide the distinct antimicrobial activities of the dimeric forms of the human defensins HNP-1, HNP-2 and HNP-3 in a membrane interface model. The present studies extend previous analyses about the structure and hydration of the HNP-3 developed, 33,34 showing a high solvent …”

Section: Introductionsupporting

confidence: 90%

Molecular dynamics study of the differences in the human defensin behavior near a modelled water/membrane interface

Namba¹,

Lourenzoni²,

Degrève³

2007

J. Braz. Chem. Soc.

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O comportamento das defensinas humanas HNP-1, HNP-2 e HNP-3 é estudado em um modelo de interface H 2 O/CCl 4 por simulações de dinâmica molecular. O comportamento distinto do HNP-3, quando comparado ao dos HNP 1 e 2, pode ser associado ao fato de o HNP-3 ser a menos potente das três defensinas, uma vez que seus resíduos apolares, que poderiam atacar as membranas celulares dos organismos patogênicos estão protegidos no interior do peptídeo. Três mecanismos encontrados na literatura propõem que a ação dos HNPs sobre membranas ocorra, principalmente, pela interação entre os seus resíduos polares e os da superfície da membrana. Esses modelos não explicam com clareza o papel da região hidrofóbica da membrana na manutenção da estrutura quaternária do dímero de HNP, quando em contato com o interior da membrana. O conhecimento do comportamento da estrutura dimérica no estágio inicial da penetração na membrana, considerando, principalmente, a natureza hidrofóbica dos HNPs, mostrou-se essencial para explicar as diferenças nas suas ações. Este trabalho contribui para o entendimento do mecanismo da ação antimicrobiana das defensinas.Human defensins HNP-1, HNP-2 and HNP-3 behavior is studied in a membrane interface model H 2 O/CCl 4 by molecular dynamics simulation. The distinct HNP-3 behavior, when compared to HNP 1 and 2, can be associated to the fact that HNP-3 is the least potent of the three defensins, since its apolar residues, which could attack the cellular membranes of the pathogenic organisms, are shielded in the inner region of the peptide. Three mechanisms were proposed to explain the HNP action on cellular membranes. These mechanisms are unable to enlighten the membrane hydrophobic part role for preserving the quaternary structure of the peptide when it is interacting with the inner part of the membrane. They suggest that the damaging is mainly caused by the interactions between the localized charges of the peptides with charges on the membrane surface. These models do not clearly explain what the hydrophobic region role is in the stabilization of the quaternary HNP structure, when it is interacting with a membrane. The understanding of how the HNP dimers structure is conserved at the first stages of the insertion into the membrane is fundamental to explain the different activities of the peptides. This work aims at contributing for the understanding of the mechanism of the defensins antimicrobial action.

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Section: Introductionsupporting

confidence: 90%

Molecular dynamics study of the differences in the human defensin behavior near a modelled water/membrane interface

Namba¹,

Lourenzoni²,

Degrève³

2007

J. Braz. Chem. Soc.

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“…For example, intramolecular hydrogen bonds are identified by interactions with a donor-receptor distance shorter than 0.24 nm, the (A-H•••O) angle larger than 110º (A≡ N or O) and the fractional occurrence larger than 20% of the total simulation time. The intermolecular hydrogen bonds can be detected by two criteria; (i) based on the radial distribution functions, g(r), and (ii) distribution of the interaction energies between the protein atoms and the solvent, F(E), (Degrève et al, 2004). The dynamics and energetic properties of MD simulations are well suited to monitor interatomic distances and angles over time, and can characterize all atom pairs involved in hydrogen bonds, hydrophobic clusters or salt bridges.…”

Section: Xylanasesmentioning

confidence: 99%

Innovations in biotechnology

Gartland

Beccari

Bruschi

et al. 2015

Journal of Biotechnology

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“…These results differ from those of Terebiznik et al (2002), who reported an improvement of the nisin (1,200 IU/mL) effect at a non-lethal PEF intensity (5 kV/cm) when the water activity of simulated milk ultrafiltrate (SMUF) decreased from 0.99 to 0.95. Since water molecules contribute to the formation of hydrogen bonds, which subsequently affect protein association and disassociation and their unspecificity (Degreve et al 2004), the difference in water activity may explain the variation in bacteriocin activity in SMUF.…”

Section: Pef and Added Nisinmentioning

confidence: 99%

Combination of Pulsed Electric Fields with Other Preservation Techniques

Martı́n-Belloso

Sobrino-López

2011

Food Bioprocess Technol

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Pulsed electric field (PEF) is a promising nonthermal treatment for liquid foods with antimicrobial activity at ambient temperature. According to the hurdle concept, the combination of PEF with other preservation methods may enhance cell death. The joint effect of PEF with the addition of antimicrobial compounds of natural origin, such as nisin, has received special attention, although other emerging nonthermal techniques, such as the use of high-pressure carbon dioxide, have also been considered. Moreover, the bactericidal action resulting from the simultaneous application of PEF and conventional thermal treatments suggests the possibility of lowering the intensity of heating while maintaining microbial acceptance. This review analyses the literature on antimicrobial strategies that combine PEF with nonthermal and traditional preservation methods. The variables affecting cell death produced by those combined treatments and their mechanisms of synergy are considered. Commercialization of PEF in combination with other technologies may be possible due to its improved antimicrobial effect.

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On the role of water in the protein activity

Cited by 10 publications

References 52 publications

Molecular dynamics study of the differences in the human defensin behavior near a modelled water/membrane interface

Molecular dynamics study of the differences in the human defensin behavior near a modelled water/membrane interface

Innovations in biotechnology

Combination of Pulsed Electric Fields with Other Preservation Techniques

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