Conformational analysis and water dynamics: a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record

Fonseca, Beatriz; Freeman, Colin L.; Collins, Matthew J.

doi:10.1016/j.chemphys.2022.111602

Cited by 3 publications

(3 citation statements)

References 46 publications

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“…Here, in contrast, it is hardly identified after extensive degradation. This suggests that the real conditions in which the peptide is found, mainly the presence of a mineral surface, contributes to its preservation, as it has been suggested using molecular simulations (Fonseca et al, 2022).…”

Section: Resultsmentioning

confidence: 57%

“…We chose BLG, as it is one of the most commonly preserved and identified proteins in dental calculus and ceramics and thus has become the main protein used in archaeology to explore the spread of dairying in the past (Bleasdale et al, 2021; Charlton et al, 2019; Gismondi et al, 2018/8; Hendy, Colonese, et al, 2018; Hendy, Warinner, et al, 2018; Jeong et al, 2018; Scott et al, 2022; Soncin et al, 2017; Tanasi et al, 2021; Warinner, Rodrigues, et al, 2014; Wilkin et al, 2021; Wilkin, Ventresca Miller, et al, 2020). It is suggested that mineral surfaces play an important role in the survival (Fonseca et al, 2022), as it has been also found for other eggshell proteins (Demarchi et al, 2016).…”

Section: Introductionmentioning

confidence: 80%

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Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

Rodriguez Palomo,

Nair,

Chiang

et al. 2023

Preprint

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Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses and interpretations of complex, degraded protein mixtures. The community has also established standards of good practice to interrogate our data. However, there is a lack of a systematic exploration of how these affect the identification of peptides, post-translational modifications (PTMs) and protein and their significance (through the False Discovery Rate) and correctness. We systematically investigated the performance of a wide range of sequencing tools and search engines in a controlled system: the experimental degradation of the single purified bovine β-lactoglobulin (BLG), heated at 95 °C and pH 7 for 0, 4 and 128 days. We target BLG since it is one of the most robust and ubiquitous proteins in the archaeological record. We tested different reference database choices, a targeted dairy protein one, and whole bovine proteome and three digestion options (tryptic-, semi-tryptic– and non-specific searches), in order to evaluate the effects of search space and the identification of peptides. We also explored alternative strategies, including open search that allows for the global identification of PTMs based upon wide precursor mass tolerance andde novosequencing to boost sequence coverage. We analysed the samples using Mascot, MaxQuant, Metamorpheus, pFind, Fragpipe and DeNovoGUI (pepNovo, DirecTag, Novor), and we benchmarked these tools and discussed the optimal strategy for the characterisation of ancient proteins.

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Section: Resultsmentioning

confidence: 57%

Section: Introductionmentioning

confidence: 80%

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

Rodriguez Palomo,

Nair,

Chiang

et al. 2023

Preprint

Self Cite

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“…For example, the TIP3P water forcefield was employed to simulate the structural and thermodynamic properties of an aqueous DNA solution [14]. The SPC/E water model can be used to explore the dynamics of peptides in bulk water [15]. The TIP4P water forcefield was used to study phase equilibria of aqueous systems [16].…”

Section: Introductionmentioning

confidence: 99%

The Magnetic Field Freezes the Mercedes–Benz Water Model

Urbic

2023

Entropy

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In this study, we investigate the impact of magnetic fields on the structural and thermodynamic properties of water. To accomplish this, we employed the Mercedes–Benz (MB) model, a two-dimensional representation of water using Lennard–Jones disks with angle-dependent interactions that closely mimic hydrogen bond formation. We extended the MB model by introducing two charges to enable interaction with the magnetic field. Employing molecular dynamics simulations, we thoroughly explored the thermodynamic properties concerning various magnetic flux intensities. As a result, we observed that under a weak magnetic flux, the property of water remained unaltered, while a stronger flux astonishingly led to the freezing of water molecules. Furthermore, our study revealed that once a specific flux magnitude was reached, the density anomaly disappeared, and an increase in flux caused the MB particles to form a glassy state.

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Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

Rodriguez Palomo,

Nair,

Chiang

et al. 2024

Peer Community Journal

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Conformational analysis and water dynamics: a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record

Cited by 3 publications

References 46 publications

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

The Magnetic Field Freezes the Mercedes–Benz Water Model

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

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