Short Peptide Sequences Research Articles

Efficiency Enhancement in Peptide Hydrogelators: The Crucial Role of Side Chain Hydrogen Bonding Over Aromatic π-π Interactions.

Short peptide assemblies that form supramolecular hydrogels are stabilized by both intermolecular noncovalent interactions among amino acid side chains and hydrogen bonding between peptide backbone amides. Previous research has emphasized the inclusion of aromatic amino acids in short peptide sequences, positing that aromatic π-π interactions contribute significantly to inducing efficient hydrogelation i.e., at low minimum gelation concentrations (MGCs). However, herein, we demonstrate that additional hydrogen bonding interactions from amino acid side chains play a more pivotal role in the efficiency of peptide hydrogelation compared to aromatic π-π interactions. We investigated two sets of Fluorenylmethoxycarbonyl (Fmoc)-functionalized α-synuclein and human islet amyloid peptide fragments [Fmoc-NVGGAVVT (Syn-N) and Fmoc-NFGAIL (IAP-N)], substituting asparagine (N) with phenylalanine (Syn-F/IAP-F), alanine (Syn-A/IAP-A), and glutamine (Syn-Q/IAP-Q). This allowed us to explore the effects of aromatic (π-system), aliphatic (hydrophobic), and hydrogen bonding effects with varying chain lengths on hydrogel formation. Our results reveal that Syn-N and Syn-Q exhibit MGC of 0.03 and 0.05 wt %, respectively, classifying them as super hydrogelators (MGC < 0.1 wt %). These values are 4.0-6.6-fold lower than Syn-F and Syn-A, with Syn-N demonstrating greater efficiency than Syn-Q. Similarly, IAP-N exhibited a substantial decrease in MGC by 8.75, 3.75, and 2.5 folds compared to IAP-A, IAP-F, and IAP-Q, respectively. Experimental evidence and molecular dynamic simulation suggest that -CO-NH2 of asparagine side chains effectively engaged in hydrogen bonding, thereby immobilizing water molecules at low gelator concentrations. Although glutamine shares similar -CO-NH2 functionality, its hydrogelation efficiency is less pronounced compared to asparagine, likely due to its longer alkyl chain, which may hinder the formation of a hydrogen bonding network in the self-assembled structure compared to asparagine-containing peptides. These findings offer valuable insights for designing efficient peptide hydrogelators or lowering MGCs by substituting amino acids with asparagine/glutamine in peptide sequences. Additionally, modifying peptide properties through asparagine/glutamine substitution could optimize hydrogel properties for specific applications.

Remarkable Stability of Glutathione-Based Supramolecular Gel in the Presence of Oxidative Stress from Hydrogen Peroxide.

Low molecular weight 7-methoxy-3-(p-nitrophenyl)iminocoumarin (MNI) with donor and acceptor groups has been synthesized. The molecule shows typical π-stacking geometry in the crystal structure. In this study, MNI, an achiral small organic molecule, forms a nanostructured supramolecular gel along with a short peptide sequence glutathione (GSH). The self-assembly of the achiral organic coumarin component and chiral biomolecule produces a chiral gel with helical fiber structures. Interestingly, the helicities of chiral gels are controlled by the solvent ratio, where MNI in DMSO and GSH in water has been used. Variation of the solvent ratio from 6:4 to 1:9 for DMSO:H2O results in six gels (4, 5, 6, 7, 8 and 9), where the gel numbers signify the water content ratio. FE-SEM analysis shows gel fibers with right-handed helical structures, which have been further confirmed by circular dichroism (CD) with notable helicity in 4 to 6. This is the first report of controlled chiral helical nanostructured supramolecular gel formation by a solvent mixture with an organic small molecule and biomolecule. Interestingly, storage modulus (G') initially decreases from 4 to 6 and further increases up to 9. An opposite strain (%) trend was observed among these six gels. These unusual solvent-dependent gel properties have been further applied to monitor the stability of the gels in the presence of hydrogen peroxide (H2O2), which converts GSH to oxidized glutathione (GSSG) in general. The oxidative stress from H2O2 disrupts 4 to 6 gels, and precipitation occurs. It is noteworthy to mention that GSSG alone cannot form a gel with the MNI molecule and forms a precipitate. Remarkably, on the other hand, 7 to 9 remain as strong gels even after H2O2 treatment. Among all six gels, 9 shows extraordinary stability of gels even after H2O2 treatment.

AlphaFold Ensemble Competition Screens Enable Peptide Binder Design with Single-Residue Sensitivity.

Understanding the relationship between the sequence and binding energy in peptide-protein interactions is an important challenge in chemical biology. A prominent example is ubiquitin interacting motifs (UIMs), which are short peptide sequences that recognize ubiquitin and which bind individual ubiquitin proteins with a weak affinity. Though the sequence characteristics of UIMs are well understood, the relationship between the sequence and ubiquitin binding affinity has not yet been fully characterized. Herein, we study the first UIM of Vps27 as a model system. Using an experimental alanine scan, we were able to rank the relative contribution of each hydrophobic residue of this UIM to ubiquitin binding. These results were correlated with AlphaFold displacement studies, in which AlphaFold is used to predict the stronger binder by presenting a target protein with two potential peptide ligands. We demonstrate that by generating large numbers of models and using the consensus bound-state AlphaFold competition experiments can be sensitive to single-residue variations. We furthermore show that to fully recapitulate the binding trends observed for ubiquitin, it is necessary to screen AlphaFold models that incorporate a "decoy" binding site to prevent the displaced peptide from interfering with the actual binding site. Overall, it is shown that AlphaFold can be used as a powerful tool for peptide binder design and that when large ensembles of models are used, AlphaFold predictions can be sensitive to very small energetic changes arising from single-residue alterations to a binder.

Developing New Peptides and Peptide-Drug Conjugates for Targeting the FGFR2 Receptor-Expressing Tumor Cells and 3D Spheroids.

In this work, we utilized a biomimetic approach for targeting KATO (III) tumor cells and 3D tumoroids. Specifically, the binding interactions of the bioactive short peptide sequences ACSAG (A-pep) and LPHVLTPEAGAT (L-pep) with the fibroblast growth factor receptor (FGFR2) kinase domain was investigated for the first time. Both peptides have been shown to be derived from natural resources previously. We then created a new fusion trimer peptide ACSAG-LPHVLTPEAGAT-GASCA (Trimer-pep) and investigated its binding interactions with the FGFR2 kinase domain in order to target the fibroblast growth factor receptor 2 (FGFR2), which is many overexpressed in tumor cells. Molecular docking and molecular dynamics simulation studies revealed critical interactions with the activation loop, hinge and glycine-rich loop regions of the FGFR2 kinase domain. To develop these peptides for drug delivery, DOX (Doxorubicin) conjugates of the peptides were created. Furthermore, the binding of the peptides with the kinase domain was further confirmed through surface plasmon resonance studies. Cell studies with gastric cancer cells (KATO III) revealed that the conjugates and the peptides induced higher cytotoxicity in the tumor cells compared to normal cells. Following confirmation of cytotoxicity against tumor cells, the ability of the conjugates and the peptides to penetrate 3D spheroids was investigated by evaluating their permeation in co-cultured spheroids grown with KATO (III) and colon tumor-associated fibroblasts (CAFs). Results demonstrated that Trimer-pep conjugated with DOX showed the highest permeation, while the ACSAG conjugate also demonstrated reasonable permeation of the drug. These results indicate that these peptides may be further explored and potentially utilized to create drug conjugates for targeting tumor cells expressing FGFR2 for developing therapeutics.

Biomimetic Hyaluronan Binding Biomaterials to Capture the Complex Regulation of Hyaluronan in Tissue Development and Function.

Within native ECM, Hyaluronan (HA) undergoes remarkable structural remodeling through its binding receptors and proteins called hyaladherins. Hyaladherins contain a group of tandem repeat sequences, such as LINK domains, BxB7 homologous sequences, or 20-50 amino acid long short peptide sequences that have high affinity towards side chains of HA. The HA binding sequences are critical players in HA distribution and regulation within tissues and potentially attractive therapeutic targets to regulate HA synthesis and organization. While HA is a versatile and successful biopolymer, most HA-based therapeutics have major differences from a native HA molecule, such as molecular weight discrepancies, crosslinking state, and remodeling with other HA binding proteins. Recent studies showed the promise of HA binding domains being used as therapeutic biomaterials for osteoarthritic, ocular, or cardiovascular therapeutic products. However, we propose that there is a significant potential for HA binding materials to reveal the physiological functions of HA in a more realistic setting. This review is focused on giving a comprehensive overview of the connections between HA's role in the body and the potential of HA binding material applications in therapeutics and regenerative medicine. We begin with an introduction to HA then discuss HA binding molecules and the process of HA binding. Finally, we discuss HA binding materials anf the future prospects of potential HA binding biomaterials systems in the field of biomaterials and tissue engineering.

Construction of Cell Membrane Chromatography Screening Materials Based on Avi-Tag Fused G Protein-Coupled Receptors.

Mas-related G protein-coupled receptor X2 (MrgprX2) plays a crucial role in anaphylactoid reactions and allergic diseases. Some antagonists with reasonable potency and selectivity have been reported. Cell membrane chromatography (CMC) is effective for discovering ligands. Protein-tag-based CMC models (e.g., SNAP tags and HALO tags) have enhanced performance but also increased nonspecific adsorption of small molecules. The Avi tag, a short peptide sequence, binds biotin specifically via BirA catalysis. Our study showed that 2-iminobiotin (IB) can be a BirA substrate, enabling the development of a new cell membrane stationary phase (CMSP) based on the chemical properties (modifying carboxyl silica gel and specifically labeling the Avi tag) of IB. First, we constructed the MrgprX2-Avi-tag HEK293T cell line. Next, we synthesized IB-modified silica gel (SiO2-IB) stepwise. Finally, we immobilized Avi-tagged MrgprX2 cell membranes on SiO2-IB under BirA catalysis. We characterized the developed CMSP and used it to establish a MrgprX2-Avi-tag/CMC-HPLC/MS two-dimensional screening platform, successfully screening vitexicarpin fromViticis Fructus extract via a 2D/CMC platform. In vitro and in vivo experiments confirmed that vitexicarpin targets the MrgprX2 receptor, demonstrating antiallergic effects. Our IB-Avi tag-based CMC approach effectively decreased nonspecific adsorption of the screening materials. The Avi-tag-based 2D/CMC platform is suitable for screening potential drug candidates.

A Short Sequence Targets Transmembrane Proteins to Primary Cilia.

Primary cilia are finger-like sensory organelles that extend from the bodies of most cell types and have a distinct lipid and protein composition from the plasma membrane. This partitioning is maintained by a diffusion barrier that restricts the entry of non-ciliary proteins, and allows the selective entry of proteins harboring a ciliary targeting sequence (CTS). However, CTSs are not stereotyped and previously reported sequences are insufficient to drive efficient ciliary localisation across diverse cell types. Here, we describe a short peptide sequence that efficiently targets transmembrane proteins to primary cilia in all tested cell types, including human neurons. We generate human-induced pluripotent stem cell (hiPSC) lines stably expressing a transmembrane construct bearing an extracellular HaloTag and intracellular fluorescent protein, which enables the bright, specific labeling of primary cilia in neurons and other cell types to facilitate studies of cilia in health and disease. We demonstrate the utility of this resource by developing an image analysis pipeline for the automated measurement of primary cilia to detect changes in their length associated with altered signaling or disease state.

Inducing α-Helicity in Peptides by Silver Coordination to Cysteine.

Short peptide sequences consisting of two cysteine residues separated by three other amino acids display complete change from random coil to α-helical secondary structure in response to addition of Ag+ ions. The folded CXXXC/Ag+ complex involves formation of multinuclear Ag+ species and is stable in a wide pH range from below 3 to above 8. The complex is stable through reversed-phase HPLC separation as well as towards a physiological level of chloride ions, based on far-UV circular dichroism spectroscopy. In electrospray MS under acidic conditions a peptide dimer with four Ag+ ions bound was observed, and modelling based on potentiometric experiments supported this to be the dominating complex at neutral pH together with a peptide dimer with 3 Ag+ and one proton at lower pH. The complex was demonstrated to work as a N-terminal nucleation site for inducing α-helicity into longer peptides. This type of silver-mediated peptide assembly and folding may be of more general use for stabilizing not only peptide folding but also for controlling oligomerization even under acidic conditions.

Insights and Advancements in Periodontal Tissue Engineering and Bone Regeneration.

The regeneration of periodontal bone defects continues to be an essential therapeutic concern in dental biomaterials. Numerous biomaterials have been utilized in this sector so far. However, the immune response and vascularity in defect regions may be disregarded when evaluating the effectiveness of biomaterials for bone repair. Among several regenerative treatments, the most recent technique of in situ tissue engineering stands out for its ability to replicate endogenous restorative processes by combining scaffold with particular growth factors. Regenerative medicine solutions that combine biomaterials/scaffolds, cells, and bioactive substances have attracted significant interest, particularly for bone repair and regeneration. Dental stem cells (DSCs) share the same progenitor and immunomodulatory properties as other types of MSCs, and because they are easily isolable, they are regarded as desirable therapeutic agents in regenerative dentistry. Recent research has demonstrated that DSCs sown on newly designed synthetic bio-material scaffolds preserve their proliferative capacity while exhibiting increased differentiation and immuno-suppressive capabilities. As researchers discovered how short peptide sequences modify the adhesion and proliferative capacities of scaffolds by activating or inhibiting conventional osteogenic pathways, the scaffolds became more effective at priming MSCs. In this review, the many components of tissue engineering applied to bone engineering will be examined, and the impact of biomaterials on periodontal regeneration and bone cellular biology/molecular genetics will be addressed and updated.

Reactivity of amino acids and short peptide sequences: identifying bioactive compounds via DFT calculations.

Bioactive peptides are short amino acid sequences that play important roles in various physiological processes, including antioxidant and protective effects. These compounds can be obtained through protein hydrolysis and have a wide range of potential applications in a variety of areas. However, despite the potential of these compounds, more in-depth knowledge is still necessary to better understand details regarding their chemical reactivity and electronic properties. In this study, we used molecular modeling techniques to investigate the electronic structure of isolated amino acids (AA) and short peptide sequences. Details on the relative alignments between the frontier electronic levels, local chemical reactivity and donor-acceptor properties of the 20 primary amino acids and some di- and tripeptides were evaluated in the framework of the density functional theory (DFT). Our results suggest that the electronic properties of isolated amino acids can be used to interpret the reactivity of short sequences. We found that aromatic and charged amino acids, as well as Methionine, play a key role in determining the local reactivity of peptides, in agreement with experimental data. Our analyses also allowed us to identify the influence of the relative position of AA and terminations on the local reactivity of the sequences, which can guide experimental studies and help to propose/evaluate possible mechanisms of action. In summary, our data indicate that the position of active sites of polypeptides can be predicted from short sequences, providing a promising strategy for the synthesis and bioprospection of new optimized compounds.

Myospreader improves gene editing in skeletal muscle by myonuclear propagation

Successful CRISPR/Cas9-based gene editing in skeletal muscle is dependent on efficient propagation of Cas9 to all myonuclei in the myofiber. However, nuclear-targeted gene therapy cargos are strongly restricted to their myonuclear domain of origin. By screening nuclear localization signals and nuclear export signals, we identify "Myospreader," a combination of short peptide sequences that promotes myonuclear propagation. Appending Myospreader to Cas9 enhances protein stability and myonuclear propagation in myoblasts and myofibers. AAV-delivered Myospreader dCas9 better inhibits transcription of toxic RNA in a myotonic dystrophy mouse model. Furthermore, Myospreader Cas9 achieves higher rates of gene editing in CRISPR reporter and Duchenne muscular dystrophy mouse models. Myospreader reveals design principles relevant to all nuclear-targeted gene therapies and highlights the importance of the spatial dimension in therapeutic development.

Exploring a Solvent Dependent Strategy to Control Self-Assembling Behavior and Cellular Interaction in Laminin-Mimetic Short Peptide based Supramolecular Hydrogels.

Self-assembled hydrogels, fabricated through diverse non-covalent interactions, have been extensively studied in regenerative medicines. Inspired from bioactive functional motifs of ECM protein, short peptide sequences have shown remarkable abilities to replicate the intrinsic features of the natural extracellular milieu. In this direction, we have fabricated two short hydrophobic bioactive sequences derived from the laminin protein i. e., IKVAV and YIGSR. Based on the substantial hydrophobicity of these peptides, we selected a co-solvent approach as a suitable gelation technique that included different concentrations of DMSO as an organic phase along with an aqueous solution containing 0.1 % TFA. These hydrophobic laminin-based bioactive peptides with limited solubility in aqueous physiological environment showed significantly enhanced solubility with higher DMSO content in water. The enhanced solubility resulted in extensive intermolecular interactions that led to the formation of hydrogels with a higher-order entangled network along with improved mechanical properties. Interestingly, by simply modulating DMSO content, highly tunable gels were accessed in the same gelator domain that displayed differential physicochemical properties. Further, the cellular studies substantiated the potential of these laminin-derived hydrogels in enhancing cell-matrix interactions, thereby reinforcing their applications in tissue engineering.

"Fluorine Effects" in Conformational Orchestration of α/β Hybrid Peptide with a 9-membered Pseudo β-Turn Motif.

Fluorine, the tiny robust atom, with its unique features has captured the attention of scientists in recent times, especially in drug discovery with its integration in small molecules, peptides, and proteins. However, studies to understand the 'fluorine effects' on the conformation of molecules that follow 'beyond the rule of 5' are in the infancy yet significant in molecular design and function. For the first time, using short hybrid peptide sequence as an appropriate model, we examined the substitution effect (size, stereoelectronic effect, and hydrogen bonding) using X-ray diffraction, 2D-NMR, and CD studies. The comparative study on their folding patterns with hydrogen-substituted analogs can provide valuable insights into fluorinated substrates' design.

A chimeric antigen receptor-based cellular safeguard mechanism for selective in vivo depletion of engineered T cells.

Adoptive immunotherapy based on chimeric antigen receptor (CAR)-engineered T cells has exhibited impressive clinical efficacy in treating B-cell malignancies. However, the potency of CAR-T cells carriethe potential for significant on-target/off-tumor toxicities when target antigens are shared with healthy cells, necessitating the development of complementary safety measures. In this context, there is a need to selectively eliminate therapeutically administered CAR-T cells, especially to revert long-term CAR-T cell-related side effects. To address this, we have developed an effective cellular-based safety mechanism to specifically target and eliminate the transferred CAR-T cells. As proof-of-principle, we have designed a secondary CAR (anti-CAR CAR) capable of recognizing a short peptide sequence (Strep-tag II) incorporated into the hinge domain of an anti-CD19 CAR. In in vitro experiments, these anti-CAR CAR-T cells have demonstrated antigen-specific cytokine release and cytotoxicity when co-cultured with anti-CD19 CAR-T cells. Moreover, in both immunocompromised and immunocompetent mice, we observed the successful depletion of anti-CD19 CAR-T cells when administered concurrently with anti-CAR CAR-T cells. We have also demonstrated the efficacy of this safeguard mechanism in a clinically relevant animal model of B-cell aplasia induced by CD19 CAR treatment, where this side effect was reversed upon anti-CAR CAR-T cells infusion. Notably, efficient B-cell recovery occurred even in the absence of any pre-conditioning regimens prior anti-CAR CAR-T cells transfer, thus enhancing its practical applicability. In summary, we developed a robust cellular safeguard system for selective in vivo elimination of engineered T cells, offering a promising solution to address CAR-T cell-related on-target/off-tumor toxicities.

What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments.

Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.

Metal co-factors to enhance catalytic activity of short prion-derived peptide sequences.

Development of biomolecular enzyme mimics to efficiently catalyse biochemical reactions are of prime relevance for the bulk scale production of industrially relevant biocatalyst. In this regard, amyloidogenic peptides act as suitable self-assembling scaffolds, providing stable nanostructures with high surface area facilitating biocatalysis. Herein, we rationally design two positional amyloidogenic peptide isomers, "Fmoc-VYYAHH (1)" and "Fmoc-VHHAYY (2)" considering catalytic and metal binding affinity of histidine and tyrosine when placed in periphery vs. inner core of the peptide sequence. With an ultimate objective of designing metalloenzyme mimic, we choose Co2+ and Cu2+ as divalent transition metal cations for peptide complexation to aid in catalysis. After optimizing self-assembly of innate peptides, we investigate metal-peptide binding ratio and co-ordination, finally selecting 1:1 peptide metal complex suitable for biocatalysis. Metallopeptides act as better catalysts than the innate peptides as acyl esterase when tyrosines were present at the periphery. Kinetic parameters for assessing hydrolysis rate were calculated by fitting data into Michaelis-Menten and Lineweaver Burk plots. Catalytic activity is altered depending on the stability of peptide metal complexes. 2-Cu acting as the best biocatalyst with a kcat/KM =0.08M/s. The protocols mentioned in this chapter meticulously cover the design, synthesis, self-assembly and enzyme kinetics.

Assembly and catalytic activity of short prion-inspired peptides.

Enzymes play a crucial role in biochemical reactions, but their inherent structural instability limits their performance in industrial processes. In contrast, amyloid structures, known for their exceptional stability, are emerging as promising candidates for synthetic catalysis. This article explores the development of metal-decorated nanozymes formed by short peptides, inspired by prion-like domains. We detail the rational design of synthetic short Tyrosine-rich peptide sequences, focusing on their self-assembly into stable amyloid structures and their metallization with biologically relevant divalent metal cations, such as Cu2+, Ni2+, Co2+ and Zn2+. The provided experimental framework offers a step-by-step guide for researchers interested in exploring the catalytic potential of metal-decorated peptides. By bridging the gap between amyloid structures and catalytic function, these hybrid molecules open new avenues for developing novel metalloenzymes with potential applications in diverse chemical reactions.

Crystal structure analysis of helix–turn–helix type motifs in α,γ-hybrid peptides

Design of helix–turn–helix type mimetics using short α,γ-hybrid peptides as helices and (E)-α,β-unsaturated γ-amino acids as conformationally rigid linkers and their conformations in single crystals are reported.

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins

BackgroundNumerous tools exist for biological sequence comparisons and search. One case of particular interest for immunologists is finding matches for linear peptide T cell epitopes, typically between 8 and 15 residues in length, in a large set of protein sequences. Both to find exact matches or matches that account for residue substitutions. The utility of such tools is critical in applications ranging from identifying conservation across viral epitopes, identifying putative epitope targets for allergens, and finding matches for cancer-associated neoepitopes to examine the role of tolerance in tumor recognition.ResultsWe defined a set of benchmarks that reflect the different practical applications of short peptide sequence matching. We evaluated a suite of existing methods for speed and recall and developed a new tool, PEPMatch. The tool uses a deterministic k-mer mapping algorithm that preprocesses proteomes before searching, achieving a 50-fold increase in speed over methods such as the Basic Local Alignment Search Tool (BLAST) without compromising recall. PEPMatch’s code and benchmark datasets are publicly available.ConclusionsPEPMatch offers significant speed and recall advantages for peptide sequence matching. While it is of immediate utility for immunologists, the developed benchmarking framework also provides a standard against which future tools can be evaluated for improvements. The tool is available at https://nextgen-tools.iedb.org, and the source code can be found at https://github.com/IEDB/PEPMatch.

Free-standing Three‐dimensional Graphene Scaffolds for Protease Functional Assay

Three-dimensional graphene scaffolds (3d-GS) of high porosity possessing good fluorescence quenching properties are potential candidates for the development of optical biosensors. Herein, we demonstrate the feasibility of utilising intact and free-standing 3d-GS for sensitive detection of proteases, a class of disease diagnosis biomarkers of significant interest. Recombinant OmpT was employed as a model protease for validating the proposed methodology. A short (15-residue) peptide sequence encoding a specific recognition site for OmpT was end-labelled with a fluorescent dye (5-FAM) whose fluorescence is quenched when the peptide is anchored to 3d-GS. However, in the presence of OmpT, the peptide is cleaved and released from 3d-GS, resulting in a significant recovery in fluorescence. The functional assay described herein involves a single step fabrication process of anchoring the peptide to 3d-GS. The integrity of the 3d-GS is hypothesised to overcome the concern of dynamic re-quenching associated with the typical homogeneous assays based on graphene, yielding a limit of detection (LOD) of ∼ 140 nM, which is over an order higher than homogeneous assays performed using the same composition of graphene in powdered form. To the best of our knowledge, this is the first report on utilising free-standing 3d-GS for facile assaying of proteases.