Biology subjects

Damry, A. M.

Publications and source records attributed to Damry, A. M..

9 recordsLinked to original sources

bioRxiv2026

Direct measurement of PET hydrolase interfacial kinetics reveals catalysis-independent surface remodelling

How PET hydrolases engage solid plastic has been inferred almost entirely from soluble analogs and surfactant-stabilised nanoparticle suspensions, and reported affinities span orders of magnitude. Here we measure it directly, depositing thin amorphous PET films onto gold surface plasmon resonance chips and following enzyme binding to authentic polymer in real time. Four PET hydrolases, LCC, LCC-ICCG, IsPETase-EHA and TfCut2, all bind with nanomolar apparent affinity and surface residence half-lives of tens of minutes. LCC-ICCG dissociates at 4.0 x 10^-1, within twofold of its kcat measured on authentic PET, indicating that turnover is limited by disengagement rather than by ester hydrolysis. During association, we observe non-monophasic responses for these enzymes, including, for several, a signal fall while enzyme is still flowing over the surface. This decline persists in a catalytically inactivated variant, is absent in control proteins and a structurally homologous non-plastic degrading cutinase, and cannot arise from movement of the bound enzyme alone. The polymer surface must therefore be altered non-catalytically by PET hydrolase binding. The process runs at different rates for different enzymes on an identical film, is suppressed by dilute Triton X-100, and is modulated biphasically by PET degradation products. Altogether, we conclude that enzymatic PET depolymerisation involves a catalysis-independent chain-mobilisation step that soluble assays cannot report.

biophysics↗

bioRxiv2025

Mapping Functional Dynamics Hotspots for Protein Engineering with NMR Peak Intensity Analysis

Structural dynamics play a crucial role in protein function, and tuning these dynamics through mutagenesis has emerged as a promising strategy for enhancing activity. However, identifying dynamics hotspots for protein engineering remains a labor-intensive challenge. Here, we demonstrate that NMR peak intensity analysis--a rapid, qualitative method with residue-level resolution--can identify functionally relevant dynamic regions with high precision. Using a family of red fluorescent proteins (RFPs) as a case study, we reveal that flexibility in specific regions of their structures correlates with function. Specifically, as quantum yield increases, the side of the {beta}-barrel closest to the chromophore phenolate moiety becomes more rigid, while the opposite side, closest to the acylimine group, gains flexibility. Notably, the phenolate face corresponds to a mutational hotspot frequently targeted in directed evolution campaigns aimed at enhancing brightness, underscoring its functional significance. B-factor analysis of non-cryogenic X-ray crystal structures further supports our findings. Our results establish NMR peak intensity analysis as a promising tool for mapping functional dynamics hotspots to guide protein engineering campaigns.

biophysics↗

bioRxiv2024

Ancestral reconstruction of polyethylene terephthalate degrading cutinases reveals a rugged and unexplored sequence-fitness landscape

The enzymatic degradation of polyethylene terephthalate (PET) is a promising method of advanced plastic recycling. Traditional protein engineering methods often fall short in exploring protein sequence space for optimal enzymes due to structural and rational design limitations. Our study addresses this by using multiplexed ancestral sequence reconstruction (mASR) to explore the evolutionary sequence space of PET-degrading cutinases. With a dataset of 397 cutinase sequences, we created a diverse library of ancestral sequences. Experimental characterization of 48 ancestral sequences revealed a wide range of PETase activities, highlighting the value of mASR in uncovering functional variants when compared to traditional ASR. Our results showed that PETase activity in cutinases evolved through diverse pathways involving distal mutations to the active site, and is readily accessible within this family. Additionally, our analysis of the PETase fitness landscape using one-hot encoding (OHE) and local ancestral sequence embedding (LASE) highlighted the effectiveness of LASE in capturing sequence features relevant to activity. This work emphasizes the utility of mASR as a protein engineering tool for identifying enhanced PET-degrading enzymes, and the advantages of the LASE embedding scheme in mapping the PETase fitness landscape.

biochemistry↗

bioRxiv2022

Computational remodeling of an enzyme conformational landscape for altered substrate selectivity

Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design. Using this method, we redesigned the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation, and thereby increase catalytic efficiency with a non-native substrate to alter substrate selectivity. Steady-state kinetics of designed variants revealed selectivity switches of up to 1900-fold, and structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirmed that conformational equilibria favoured the target conformation. Our computational approach opens the door to the fine-tuning of enzyme conformational landscapes to create designer biocatalysts with tailored functionality.

biophysics↗

bioRxiv2021

Electrodetection of small molecules by conformation-mediated signal enhancement

Electrochemical biosensors allow the rapid, selective, and sensitive transduction of critical biological parameters into measurable signals. However, current electrochemical biosensors often fail to selectively and sensitively detect small molecules due to their small size and low molecular complexity. We have developed an electrochemical biosensing platform that harnesses the analyte-dependent conformational change of highly selective solute-binding proteins to amplify the signal generated by analyte binding. Using this platform, we constructed and characterized two biosensors that can sense leucine and glycine, respectively. We show that these biosensors can selectively and sensitively detect their targets over a wide range of concentrations - up to seven orders of magnitude - and that the selectivity of these sensors can be readily altered by switching the bioreceptors binding domain. Our work represents a new paradigm for the design of a family of modular electrochemical biosensors, where access to electrode surfaces can be controlled by protein conformational change.

biochemistry↗

bioRxiv2021

Structural and functional characterization of a putative de novo gene in Drosophila

Comparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from non-coding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and CD data, we show that Goddard protein contains a large central -helix, but is otherwise partially disordered. We find similar results for Goddards orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddards structure appears to have been maintained with only minor changes over millions of years.

evolutionary biology↗

bioRxiv2020

Consensus mutagenesis and ancestral reconstruction provide insight into the substrate specificity and evolution of the front-end Δ6-desaturase family

Marine algae are a major source of omega ({omega})-3 long-chain polyunsaturated fatty acids ({omega}3-LCPUFAs), which are conditionally essential nutrients in humans and a target for industrial production. The biosynthesis of these molecules in marine algae begins with the desaturation of fatty acids by {Delta}6-desaturases and enzymes from different species display a range of specificities towards {omega}3 and {omega}6 LCPUFAs. In the absence of a molecular structure, the structural basis for the variable substrate specificity of {Delta}6-desaturases is poorly understood. Here we have conducted a consensus mutagenesis and ancestral protein reconstruction-based analysis of the {Delta}6-desaturase family, focusing on the {omega}3-specific {Delta}6-desaturase from Micromonas pusilla (Mp{Delta}6des) and the bispecific ({omega}3/{omega}6) {Delta}6-desaturase from Ostreococcus tauri (Ot{Delta}6des). Our characterization of consensus amino acid substitutions in Mp{Delta}6des revealed that residues in diverse regions of the protein, such as the N-terminal cytochrome b5 domain, can make important contributions to determining substrate specificity. Ancestral protein reconstruction also suggests that some extant {Delta}6-desaturases, such as Ot{Delta}6des, could have adapted to different environmental conditions by losing specificity for {omega}3-LCPUFAs. This dataset provides a map of regions within {Delta}6-desaturases that contribute to substrate specificity and could facilitate future attempts to engineer these proteins for use in biotechnology.

biochemistry↗

bioRxiv2019

Origin of Conformational Dynamics in a Globular Protein

Protein structures are dynamic, undergoing specific motions that can play a vital role in function. However, the link between primary sequence and conformational dynamics remains poorly understood. Here, we studied how conformational dynamics can arise in a globular protein by evaluating the impact of individual substitutions of core residues in DANCER-3, a streptococcal protein G domain {beta}1 (G{beta}1) variant that we previously designed to undergo a specific mode of conformational exchange that has never been observed in the wild-type protein. Using a combination of solution NMR experiments and molecular dynamics simulations, we demonstrate that only two mutations are necessary to create this conformational exchange, and that these mutations work synergistically, with one destabilizing the native G{beta}1 structure and the other allowing two new conformational states to be accessed on the energy landscape. Overall, our results show how conformational dynamics can appear in a stable globular fold, a critical step in the molecular evolution of new dynamics-linked functions.

biophysics↗

bioRxiv2017

Rational design of proteins that exchange on functional timescales

Proteins are intrinsically dynamic molecules that can exchange between multiple conformational states, enabling them to carry out complex molecular processes with extreme precision and efficiency. Attempts to design novel proteins with tailored functions have mostly failed to yield efficiencies matching those found in nature because standard methods do not allow for the design of exchange between necessary conformational states on a functionally-relevant timescale. Here, we develop a broadly-applicable computational method to engineer protein dynamics that we term meta-multistate design. We used this methodology to design spontaneous exchange between two novel conformations introduced into the global fold of Streptococcal protein G domain {beta}1. The designed proteins, named DANCERs, for Dynamic And Native Conformational ExchangeRs, are stably folded and exchange between predicted conformational states on the millisecond timescale. The successful introduction of defined dynamics on functional timescales opens the door to new applications requiring a protein to spontaneously access multiple conformational states.

biophysics↗