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Silica-binding peptides: physical chemistry and emerging biomaterials applications

IOP Publishing
Journal of Physics: Condensed Matter
Authors:
Wilson Tárraga at National Scientific and Technical Research Council
Wilson Tárraga
Marilina Cathcarth at National University of La Plata
Marilina Cathcarth
Agustin S Picco at National University of La Plata
Agustin S Picco
Gabriel S Longo at National University of La Plata
Gabriel S Longo
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Abstract and Figures

Silica-binding peptides (SBPs) are increasingly recognized as versatile tools for various applications spanning biosensing, biocatalysis, and environmental remediation. This review explores the interaction between these peptides and silica surfaces, offering insights into how variables such as surface silanol density, peptide sequence and composition, and solution conditions influence binding affinity. Key advancements in SBP applications are discussed, including their roles in protein purification, biocatalysis, biosensing, and biomedical engineering. By examining the underlying binding mechanisms and exploring their practical potential, this work provides a comprehensive understanding of how SBPs can drive innovations in materials science and biotechnology.
Influence of silanol group types, pH, and salt concentration on the electric properties of the silica surface. Panel (A): representation of the silica surface. Panel (B): illustration of the acid-base equilibria of surface silanol groups, depicting protonated, neutral, and siloxide forms, along with molecular structures of vicinal, isolated, and geminal silanols. Panels (A) and (B) Reproduced from [63], with permission from Springer Nature. Panel (C): theoretical prediction: surface charge density as a function of pH for different silanol densities, σOH (the model uses a single pKa = 6.5). The surface charge increases with both solution pH and the surface density of silanol groups. Panel (D): theoretical calculation: surface charge density as a function of pH for different salt concentrations. Increasing salt concentration ( Csalt= 1, 10, and 100 mM NaCl) results in a more negatively charged surface. The surface charge density at all conditions is much less negative as compared to the isolated silanol groups (dotted line). Panels (C) and (D) Reproduced from [69]. ©IOP Publishing Ltd. All rights reserved.
Influence of silanol group types, pH, and salt concentration on the electric properties of the silica surface. Panel (A): representation of the silica surface. Panel (B): illustration of the acid-base equilibria of surface silanol groups, depicting protonated, neutral, and siloxide forms, along with molecular structures of vicinal, isolated, and geminal silanols. Panels (A) and (B) Reproduced from [63], with permission from Springer Nature. Panel (C): theoretical prediction: surface charge density as a function of pH for different silanol densities, σOH (the model uses a single pKa = 6.5). The surface charge increases with both solution pH and the surface density of silanol groups. Panel (D): theoretical calculation: surface charge density as a function of pH for different salt concentrations. Increasing salt concentration ( Csalt= 1, 10, and 100 mM NaCl) results in a more negatively charged surface. The surface charge density at all conditions is much less negative as compared to the isolated silanol groups (dotted line). Panels (C) and (D) Reproduced from [69]. ©IOP Publishing Ltd. All rights reserved.
… 
Driving force for the adsorption of peptides onto silica and the impact of medium conditions, pH, and salt concentration. Panel (A): correlation between peptide isoelectric point and the minimal initial peptide concentration required for adsorption, [pep]min, for different peptides (7mer: LDHSLHS, pep2: YITPYAHLRGGN, pep1: KSLSRHDHIHHH, pep4: MHRSDLMSAAVR, Si4-1: MSPHPHRHHHT, Si4-10: RGRRRRLSCRLL) (50 mM phosphate, 150 mM NaCl, pH 7.5). Reprinted with permission from [24]. Copyright (2012) American Chemical Society. Panel (B): amount of adsorbed peptides on silica NPs as a function of the solution pH for KLPGWSG, AFILPTG, and LDHSLHS (buffer 100 mM phosphate, 150 mM NaCl). Reprinted with permission from [115]. Copyright (2014) American Chemical Society. Panel (C): influence of NaCl concentration on the SPR shift by the adsorption of sfGFP-Car9 (Car9: DSARGFKKPGKR) construct onto silica substrates (buffer 20 mM Tris-HCl with 0, 50, and 100 mM NaCl, pH 7.5, 0.125 µM sfGFP-Car9). Reprinted with permission from [25]. Copyright (2019) American Chemical Society.
Driving force for the adsorption of peptides onto silica and the impact of medium conditions, pH, and salt concentration. Panel (A): correlation between peptide isoelectric point and the minimal initial peptide concentration required for adsorption, [pep]min, for different peptides (7mer: LDHSLHS, pep2: YITPYAHLRGGN, pep1: KSLSRHDHIHHH, pep4: MHRSDLMSAAVR, Si4-1: MSPHPHRHHHT, Si4-10: RGRRRRLSCRLL) (50 mM phosphate, 150 mM NaCl, pH 7.5). Reprinted with permission from [24]. Copyright (2012) American Chemical Society. Panel (B): amount of adsorbed peptides on silica NPs as a function of the solution pH for KLPGWSG, AFILPTG, and LDHSLHS (buffer 100 mM phosphate, 150 mM NaCl). Reprinted with permission from [115]. Copyright (2014) American Chemical Society. Panel (C): influence of NaCl concentration on the SPR shift by the adsorption of sfGFP-Car9 (Car9: DSARGFKKPGKR) construct onto silica substrates (buffer 20 mM Tris-HCl with 0, 50, and 100 mM NaCl, pH 7.5, 0.125 µM sfGFP-Car9). Reprinted with permission from [25]. Copyright (2019) American Chemical Society.
… 
Impact of peptide conformation and flexibility on the adsorption behavior on silica surfaces. Panel (A): scheme of the suggested interaction of peptide LK14 (Ac-LKKLLKLKLLKLK-NH2) with a negatively charged silica surface. The peptide maintains an amphiphilic α-helix structure with charged lysine and hydrophobic leucine residues on opposite sides. Reprinted with permission from [138]. Copyright (2009) American Chemical Society. Panel (B): (Top) Ramachandran plots for peptides S1 (PPPWLPYMPPWS), S2 (LPDWWPPPQLYH), and W1 (EVRKEVVAVARN) in solution generated from MD trajectories. Peptide W1 explore more φ and ψ angles compared to S1 and S2, which indicates more configurational sampling. (Bottom) Snapshots of peptides interacting with a quartz (100) surface from the strongest binding MD trajectories. Peptides S1 and S2 exhibit stronger surface interactions compared to W1 (key interacting residues are highlighted). Reprinted with permission from [26]. Copyright (2010) American Chemical Society. Panel (C): (Left) adsorption of peptides pep1 (KSLSRHDHIHHH) and its mutant variants pep1_6 (KSLSRADHIHHH) and pep1_11 (KSLSRHDHIHAH). The adsorption order is pep1_6 > pep1 > pep1_11 for initial peptide concentrations up to 2 mg ml⁻¹ (pH 7.5, 100 mM phosphate, 150 mM NaCl). (Right) Scheme of peptide interactions with a negatively charged silica surface, showing the impact of His-6 and His-11 mutations on backbone flexibility and binding strength. Reprinted with permission from [24]. Copyright (2012) American Chemical Society.
Impact of peptide conformation and flexibility on the adsorption behavior on silica surfaces. Panel (A): scheme of the suggested interaction of peptide LK14 (Ac-LKKLLKLKLLKLK-NH2) with a negatively charged silica surface. The peptide maintains an amphiphilic α-helix structure with charged lysine and hydrophobic leucine residues on opposite sides. Reprinted with permission from [138]. Copyright (2009) American Chemical Society. Panel (B): (Top) Ramachandran plots for peptides S1 (PPPWLPYMPPWS), S2 (LPDWWPPPQLYH), and W1 (EVRKEVVAVARN) in solution generated from MD trajectories. Peptide W1 explore more φ and ψ angles compared to S1 and S2, which indicates more configurational sampling. (Bottom) Snapshots of peptides interacting with a quartz (100) surface from the strongest binding MD trajectories. Peptides S1 and S2 exhibit stronger surface interactions compared to W1 (key interacting residues are highlighted). Reprinted with permission from [26]. Copyright (2010) American Chemical Society. Panel (C): (Left) adsorption of peptides pep1 (KSLSRHDHIHHH) and its mutant variants pep1_6 (KSLSRADHIHHH) and pep1_11 (KSLSRHDHIHAH). The adsorption order is pep1_6 > pep1 > pep1_11 for initial peptide concentrations up to 2 mg ml⁻¹ (pH 7.5, 100 mM phosphate, 150 mM NaCl). (Right) Scheme of peptide interactions with a negatively charged silica surface, showing the impact of His-6 and His-11 mutations on backbone flexibility and binding strength. Reprinted with permission from [24]. Copyright (2012) American Chemical Society.
… 
Peptide–peptide association and binding on silica surfaces. Top panel illustrates the interaction of the charge-neutral peptide AFILPTG with other peptides and the silica surface at pH 7; the qualitative adsorption behavior depends on peptide concentration. The scheme highlights the influence of van der Waals interactions as peptide concentration increases. The bottom graph shows adsorption isotherms comparing the binding behavior of three different peptides on SiO2 (82 nm): S1 (KLPGWSG, circles), S2 (AFILPTG, triangles), and S3 (LDHSLHS, squares). The dotted line indicates hypothetical 100% adsorption for reference. Reprinted with permission from [114]. Copyright (2012) American Chemical Society.
Peptide–peptide association and binding on silica surfaces. Top panel illustrates the interaction of the charge-neutral peptide AFILPTG with other peptides and the silica surface at pH 7; the qualitative adsorption behavior depends on peptide concentration. The scheme highlights the influence of van der Waals interactions as peptide concentration increases. The bottom graph shows adsorption isotherms comparing the binding behavior of three different peptides on SiO2 (82 nm): S1 (KLPGWSG, circles), S2 (AFILPTG, triangles), and S3 (LDHSLHS, squares). The dotted line indicates hypothetical 100% adsorption for reference. Reprinted with permission from [114]. Copyright (2012) American Chemical Society.
… 
SBP-protein applications. Panel (A): use of SBPs for protein purification. (Left) Schematic illustration depicting the rapid and efficient purification of GFP-Car9 using a silica bead column via FPLC. SDS-PAGE results showing the elution of GFP-SBP using a lysine-containing buffer. (Right) Fraction of free protein (GFP and GFP-Car9) after incubation with silica gel beads, demonstrating the efficient attachment of the protein to silica via the Car9 modification. Reprinted from [18] John Wiley & Sons. © 2014 Wiley Periodicals, Inc. Panel (B): use of SBPs for biocatalysis in bioproduction. (Left) Illustration of the TAL-SiBP2 construct and its role in producing p-Coumaric acid. (Right) Reusability of immobilized TAL-SiBP2 under alkaline conditions, evaluated as the percentage of enzyme activity relative to the number of system uses. Reprinted from [170], Copyright (2022), with permission from Elsevier. Panel (C): use SBPs for bioremediation. (Left) Scheme of the SUP-SBP construct used for capturing uranyl ions. (Right) Reusability of the system. Reprinted with permission from [173]. Copyright (21) American Chemical Society.
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SBP-protein applications. Panel (A): use of SBPs for protein purification. (Left) Schematic illustration depicting the rapid and efficient purification of GFP-Car9 using a silica bead column via FPLC. SDS-PAGE results showing the elution of GFP-SBP using a lysine-containing buffer. (Right) Fraction of free protein (GFP and GFP-Car9) after incubation with silica gel beads, demonstrating the efficient attachment of the protein to silica via the Car9 modification. Reprinted from [18] John Wiley & Sons. © 2014 Wiley Periodicals, Inc. Panel (B): use of SBPs for biocatalysis in bioproduction. (Left) Illustration of the TAL-SiBP2 construct and its role in producing p-Coumaric acid. (Right) Reusability of immobilized TAL-SiBP2 under alkaline conditions, evaluated as the percentage of enzyme activity relative to the number of system uses. Reprinted from [170], Copyright (2022), with permission from Elsevier. Panel (C): use SBPs for bioremediation. (Left) Scheme of the SUP-SBP construct used for capturing uranyl ions. (Right) Reusability of the system. Reprinted with permission from [173]. Copyright (21) American Chemical Society.
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Journal of Physics: Condensed Matter
J. Phys.: Condens. Matter 37 (2025) 203001 (23pp) https://doi.org/10.1088/1361-648X/adc6e2
Topical Review
Silica-binding peptides: physical
chemistry and emerging biomaterials
applications
Wilson A Tárraga, Marilina Cathcarth, Agustin S Picco∗
and Gabriel S Longo∗
Instituto de Investigaciones Fisicoquímicas, Teóricas y Aplicadas (INIFTA), UNLP-CONICET, La Plata,
Argentina
E-mail: apicco@inifta.unlp.edu.ar and longogs@sica.unlp.edu.ar
Received 2 December 2024, revised 24 February 2025
Accepted for publication 28 March 2025
Published 23 April 2025
Abstract
Silica-binding peptides (SBPs) are increasingly recognized as versatile tools for various
applications spanning biosensing, biocatalysis, and environmental remediation. This review
explores the interaction between these peptides and silica surfaces, offering insights into how
variables such as surface silanol density, peptide sequence and composition, and solution
conditions inuence binding afnity. Key advancements in SBP applications are discussed,
including their roles in protein purication, biocatalysis, biosensing, and biomedical
engineering. By examining the underlying binding mechanisms and exploring their practical
potential, this work provides a comprehensive understanding of how SBPs can drive innovations
in materials science and biotechnology.
Keywords: silica-binding peptides, silica surfaces, peptide-surface interactions,
biomaterials design, biosilicication, SBPs
1. Introduction
Silica, valued for its high surface area, tunable porosity, and
exceptional chemical and thermal stability, has become widely
used across diverse elds [1–4]. These characteristics, along
with its biocompatibility and versatile surface functionaliza-
tion options, make silica-based materials especially suitable
for applications in drug delivery, catalysis, environmental
remediation, and biosensing [5–7]. For instance, mesoporous
silica nanoparticles (NPs) are widely used in drug delivery sys-
tems for their ability to host and release large amounts of thera-
peutic agents [8–13]. In environmental applications, the tun-
able surface properties and high adsorption capacity of silica
have proven effective for pollutant removal and wastewater
∗Authors to whom any correspondence should be addressed.
treatment [2]. Due to their biocompatibility and capacity to
be functionalized for specic interactions, silica nanoparticles
are increasingly integrated into diagnostic platforms and thera-
peutic systems [4,14].
The abundance of this material, along with its biocompatib-
ility, chemical versatility, and broad range of potential applic-
ations, has created a demand for precise and stable function-
alizations of silica surfaces [1–3,15]. Silica-binding peptides
(SBPs) have recently gained signicant relevance due to their
unique ability to specically bind to silica surfaces [16]. SBPs
are valuable tools in a wide array of applications, from envir-
onmental sensing and protein purication to catalysis and bio-
medical engineering [17–21].
Biotechnology enables the design of SBPs tailored to spe-
cic applications [16,22,23]. By optimizing the sequence
and structure of these peptides, researchers have developed
1
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