Application of molecular dynamic simulation to study food proteins: A review

Singh, Ashutosh; Vanga, Sai Kranthi; Orsat, Valérie; Raghavan, Vijaya

doi:10.1080/10408398.2017.1341864

Cited by 63 publications

(52 citation statements)

References 79 publications

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“…Through the years, many methods, such as nuclear magnetic resonance (NMR) and X-ray diffraction (XRD), have been extensively used to understand protein structure and the relation to its functionality. However, to fully understand the mechanism of the interactions between processing conditions and proteins, it is increasingly important to explore and comprehend the effect on properties at the molecular or even atomic level [ 139 ].…”

Section: Techniques To Quantify Astringencymentioning

confidence: 99%

Sensorial Perception of Astringency: Oral Mechanisms and Current Analysis Methods

Pires¹,

Pastrana²,

Fuciños³

et al. 2020

Foods

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Understanding consumers’ food choices and the psychological processes involved in their preferences is crucial to promote more mindful eating regulation and guide food design. Fortifying foods minimizing the oral dryness, rough, and puckering associated with many functional ingredients has been attracting interest in understanding oral astringency over the years. A variety of studies have explored the sensorial mechanisms and the food properties determining astringency perception. The present review provides a deeper understanding of astringency, a general view of the oral mechanisms involved, and the exciting variety of the latest methods used to direct and indirectly quantify and simulate the astringency perception and the specific mechanisms involved.

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Section: Techniques To Quantify Astringencymentioning

confidence: 99%

Sensorial Perception of Astringency: Oral Mechanisms and Current Analysis Methods

Pires¹,

Pastrana²,

Fuciños³

et al. 2020

Foods

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“…The MD simulation, in this regard, is a promising tool that has been widely applied to investigate the performance of complex nano-sized systems bridging diverse areas of cell biology and materials science. 48,49 Besides the great ability that the MD offers to evaluate the thermal and mechanical features of nanostructures. [50][51][52][53][54][55] The 13-amino acid peptide (named HA-FD-13) with the ID code of 2l24 (chosen from protein data bank (https://www.rcsb.org/structure/2L24)) is an α-Helical antimicrobial peptide (α-AMP) derived from the fusion domain (FD) of the hemagglutinin (HA) of the influenza virus.…”

Section: Introductionmentioning

confidence: 99%

α-Helical Antimicrobial Peptide Encapsulation and Release from Boron Nitride Nanotubes: A Computational Study

Dehaghani

Yousefi

Bagheri

et al. 2021

IJN

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Introduction Antimicrobial peptides are potential therapeutics as anti-bacteria, anti-viruses, anti-fungi, or anticancers. However, they suffer from a short half-life and drug resistance which limit their long-term clinical usage. Methods Herein, we captured the encapsulation of antimicrobial peptide HA-FD-13 into boron nitride nanotube (BNNT) (20,20) and its release due to subsequent insertion of BNNT (14,14) with molecular dynamics simulation. Results The peptide-BNNT (20,20) van der Waals (vdW) interaction energy decreased to −270 kcal·mol −1 at the end of the simulation (15 ns). However, during the period of 0.2–1.8 ns, when half of the peptide was inside the nanotube, the encapsulation was paused due to an energy barrier in the vicinity of BNNT and subsequently the external intervention, such that the self-adjustment of the peptide allowed full insertion. The free energy of the encapsulation process was −200.12 kcal·mol −1 , suggesting that the insertion procedure occurred spontaneously. Discussion Once the BNNT (14,14) entered into the BNNT (20,20), the peptide was completely released after 83.8 ps. This revealed that the vdW interaction between the BNNT (14,14) and BNNT (20,20) was stronger than between BNNT (20,20) and the peptide; therefore, the BNNT (14,14) could act as a piston pushing the peptide outside the BNNT (20,20). Moreover, the sudden drop in the vdW energy between nanotubes to the value of the −1300 Kcal·mol −1 confirmed the self-insertion of the BNNT (14,14) into the BNNT (20,20) and correspondingly the release of the peptide.

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“…To date, MD simulations applied to foods have been successfully utilized to examine lipid phase transitions and lipid‐related interactions. In food enzyme and protein research, MD simulations have served to enhance the understanding of the role of catalytic sites on the enzymatic reaction mechanisms (Mcgeagh, Ranaghan, & Mulholland, ; Reddy & Bruice, ; Singh, Vanga, Orsat, & Raghavan, ), which have produced key benefits for the redesign of specific enzymes (Liu & Wang, ). In food carbohydrates, the applications of MD simulations have been discussed in terms of the interactions between carbohydrate molecules and other components (Feng et al., ).…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

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Application of molecular dynamic simulation to study food proteins: A review

Cited by 63 publications

References 79 publications

Sensorial Perception of Astringency: Oral Mechanisms and Current Analysis Methods

Sensorial Perception of Astringency: Oral Mechanisms and Current Analysis Methods

α-Helical Antimicrobial Peptide Encapsulation and Release from Boron Nitride Nanotubes: A Computational Study

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

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