Heightened Cold-Denaturation of Proteins at the Ice–Water Interface

Arsiccio, Andrea; McCarty, James; Pisano, Roberto; Shea, Joan–Emma

doi:10.1021/jacs.9b13454

Cited by 75 publications

(37 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While it was first thought that adsorption onto the ice surface may be key for destabilization, 14 , 18 recent experimental and simulation results indicate that direct interaction with the interface is not needed. 19 − 23 In contrast, pressure build-up, 21 concentration gradients and pH shifts, 21 accumulation of gas bubbles, 24 , 25 or cold denaturation phenomena 22 were proposed as possible routes of denaturation upon ice formation. The addition of excipients to the protein formulation is therefore needed to prevent undesired loss of therapeutic potency and preserve the monomeric native conformation of the protein during both production and storage.…”

Section: Introductionmentioning

confidence: 99%

The Role of Cyclodextrins against Interface-Induced Denaturation in Pharmaceutical Formulations: A Molecular Dynamics Approach

et al. 2021

Self Cite

View full text Add to dashboard Cite

Protein-based pharmaceutical products are subject to a variety of environmental stressors, during both production and shelf-life. In order to preserve their structure, and, therefore, functionality, it is necessary to use excipients as stabilizing agents. Among the eligible stabilizers, cyclodextrins (CDs) have recently gained interest in the scientific community thanks to their properties. Here, a computational approach is proposed to clarify the role of β-cyclodextrin (βCD) and 2-hydroxypropyl-β-cyclodextrin (HPβCD) against granulocyte colony-stimulating (GCSF) factor denaturation at the air–water and ice–water interfaces, and also in bulk water at 300 or 260 K. Both traditional molecular dynamics (MD) simulations and enhanced sampling techniques (metadynamics, MetaD) are used to shed light on the underlying molecular mechanisms. Bulk simulations revealed that CDs were preferentially included within the surface hydration layer of GCSF, and even included some peptide residues in their hydrophobic cavity. HPβCD was able to stabilize the protein against surface-induced denaturation in proximity of the air–water interface, while βCD had a destabilizing effect. No remarkable conformational changes of GCSF, or noticeable effect of the CDs, were instead observed at the ice surface. GCSF seemed less stable at low temperature (260 K), which may be attributed to cold-denaturation effects. In this case, CDs did not significantly improve conformational stability. In general, the conformationally altered regions of GCSF seemed not to depend on the presence of excipients that only modulated the extent of destabilization with either a positive or a negative effect.

show abstract

Section: Introductionmentioning

confidence: 99%

The Role of Cyclodextrins against Interface-Induced Denaturation in Pharmaceutical Formulations: A Molecular Dynamics Approach

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Other experimental considerations, such as icesheet buckling during vitrification, can cause further perturbations to the observed structural ensemble. It remains to be fully assessed how much the freezing process affects the extracted free energy 56 . On the other hand, to obtain high-resolution reconstructions, it is common to set the system at temperatures below the ambient one for over stabilizing a single state.…”

Section: Discussionmentioning

confidence: 99%

A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments

Giraldo-Barreto

Ortiz

Thiede

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature it has the potential to provide information about a biomolecule’s conformational variability and underlying free-energy landscape. However, treating cryo-EM as a single-molecule technique is challenging because of the low signal-to-noise ratio (SNR) in individual particles. In this work, we propose the cryo-BIFE method (cryo-EM Bayesian Inference of Free-Energy profiles), which uses a path collective variable to extract free-energy profiles and their uncertainties from cryo-EM images. We test the framework on several synthetic systems where the imaging parameters and conditions were controlled. We found that for realistic cryo-EM environments and relevant biomolecular systems, it is possible to recover the underlying free energy, with the pose accuracy and SNR as crucial determinants. We then use the method to study the conformational transitions of a calcium-activated channel with real cryo-EM particles. Interestingly, we recover not only the most probable conformation (used to generate a high-resolution reconstruction of the calcium-bound state) but also a metastable state that corresponds to the calcium-unbound conformation. As expected for turnover transitions within the same sample, the activation barriers are on the order of $$k_BT$$ k B T . We expect our tool for extracting free-energy profiles from cryo-EM images to enable more complete characterization of the thermodynamic ensemble of biomolecules.

show abstract

“…The functional properties of meat proteins, such as the interaction between protein and protein, protein and water, and protein and fat, are very important factors in determining the quality of comminuted meat products ( Sun and Holley, 2011 ). Since the free energy barrier for protein unfolding is decreased at the ice-water interface under low temperatures, structural modification occurs during freeze-storage ( Arsiccio et al, 2020 ). Moreover, proteins can be denatured by increasing the solute concentration in unfrozen water ( Estévez et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%