The interaction of proteins with silica surfaces. Part II: Free energies of capped amino acids

Trachta, Michal; Bludský, Ota; Rubeš, Miroslav

doi:10.1016/j.comptc.2018.12.013

Cited by 4 publications

(4 citation statements)

References 47 publications

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“…Furthermore, the co-existence of organic matter and metals exacerbate particle fouling compared to solutions in which only organic matter or metals are present [ 79 , 80 ]. In a solution containing silica and bovine serum albumin (BSA), silica bonded to amino acid groups in BSA and formed a complex that increased fouling [ 81 ]. Such synergistic effects necessitate the evaluation of the antifouling performance of membranes for feed water containing a mixture of foulants.…”

Section: Reverse Osmosismentioning

confidence: 99%

Frontiers of Membrane Desalination Processes for Brackish Water Treatment: A Review

et al. 2021

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Climate change, population growth, and increased industrial activities are exacerbating freshwater scarcity and leading to increased interest in desalination of saline water. Brackish water is an attractive alternative to freshwater due to its low salinity and widespread availability in many water-scarce areas. However, partial or total desalination of brackish water is essential to reach the water quality requirements for a variety of applications. Selection of appropriate technology requires knowledge and understanding of the operational principles, capabilities, and limitations of the available desalination processes. Proper combination of feedwater technology improves the energy efficiency of desalination. In this article, we focus on pressure-driven and electro-driven membrane desalination processes. We review the principles, as well as challenges and recent improvements for reverse osmosis (RO), nanofiltration (NF), electrodialysis (ED), and membrane capacitive deionization (MCDI). RO is the dominant membrane process for large-scale desalination of brackish water with higher salinity, while ED and MCDI are energy-efficient for lower salinity ranges. Selective removal of multivalent components makes NF an excellent option for water softening. Brackish water desalination with membrane processes faces a series of challenges. Membrane fouling and scaling are the common issues associated with these processes, resulting in a reduction in their water recovery and energy efficiency. To overcome such adverse effects, many efforts have been dedicated toward development of pre-treatment steps, surface modification of membranes, use of anti-scalant, and modification of operational conditions. However, the effectiveness of these approaches depends on the fouling propensity of the feed water. In addition to the fouling and scaling, each process may face other challenges depending on their state of development and maturity. This review provides recent advances in the material, architecture, and operation of these processes that can assist in the selection and design of technologies for particular applications. The active research directions to improve the performance of these processes are also identified. The review shows that technologies that are tunable and particularly efficient for partial desalination such as ED and MCDI are increasingly competitive with traditional RO processes. Development of cost-effective ion exchange membranes with high chemical and mechanical stability can further improve the economy of desalination with electro-membrane processes and advance their future applications.

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Section: Reverse Osmosismentioning

confidence: 99%

Frontiers of Membrane Desalination Processes for Brackish Water Treatment: A Review

et al. 2021

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“…Because of such complexity, one can find different strategies to computationally model protein/surface systems. On one hand, there is the use of simplified biological systems, for example, oligopeptides with a reduced number of residues, − single amino acids, − or even amino acid analogues. − This allows adopting high-quality ab initio methods and to focus on the specific contribution of the various constituting components in the interaction. However, a biological system is not a mere collection of simplified monomers, and accordingly, this modeling approach overlooks long-ranged and cooperative effects that can greatly contribute to the stability of the protein/surface systems.…”

Section: Introductionmentioning

confidence: 99%

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO₂ (101) Anatase Surface Adopting a Full Periodic Approach

Pantaleone

Rimola

Ugliengo

et al. 2021

J. Chem. Inf. Model.

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Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO 2 (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO 2 surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO 2 surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C O groups form Ti−OC dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti−OC bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.

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“…In this rapidly advancing field, modeling is crucial for understanding at molecular-level the interactions of biomolecules with silica [2,40] in the presence of water. Indeed, theoretical studies on proteins at silica interfaces have experienced an impressive growth in the last few years [2,41,42,43,44], uncovering important microscopic features of the interaction with flat surfaces. The simulation of lysozyme [45,46], papain [47], and fragments of various proteins [48,49,50] on silica surfaces, for instance, revealed conformational changes, and in some cases even a certain degree of unfolding of the biomolecule upon surface adhesion.…”

Section: Introductionmentioning

confidence: 99%

“…In a different way, a more accurate description may be obtained by considering amino acid molecules on silica surfaces, and, more recently, in MCM-41 pores, for which quantum chemical methods can be employed [2,51]. Several quantum chemistry and experimental investigations have highlighted significant interactions of amino acids, drugs, and other organic species in contact with SiO 2 -surfaces [41,52,53,54,55,56]. Also, first principles molecular dynamics of nanoconfined organic molecules has enabled a deeper understanding of the key influence of water on the stability of hybrid functional materials [57,58,59,60].…”

Section: Introductionmentioning

confidence: 99%

Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels

Giussani

Tabacchi

Coluccia

et al. 2019

IJMS

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Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas.

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The interaction of proteins with silica surfaces. Part II: Free energies of capped amino acids

Cited by 4 publications

References 47 publications

Frontiers of Membrane Desalination Processes for Brackish Water Treatment: A Review

Frontiers of Membrane Desalination Processes for Brackish Water Treatment: A Review

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO₂ (101) Anatase Surface Adopting a Full Periodic Approach

Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels

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The interaction of proteins with silica surfaces. Part II: Free energies of capped amino acids

Cited by 4 publications

References 47 publications

Frontiers of Membrane Desalination Processes for Brackish Water Treatment: A Review

Frontiers of Membrane Desalination Processes for Brackish Water Treatment: A Review

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach

Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels

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First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO₂ (101) Anatase Surface Adopting a Full Periodic Approach