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Publications (80)
Bacterial microcompartments (BMC) are submicrometric reactors that encapsulate dedicated metabolic activities. BMC-H hexamers, the most abundant components of BMC shells, play major roles for shell plasticity and permeability. In part, chemical exchanges between the BMC lumen and the cellular cytosol will be defined by the disposition of amino acid...
Proteins, the fundamental building blocks of biological function, orchestrate complex cellular processes by assembling into intricate structures through meticulous interactions. The design of specific protein-protein interfaces to create customized protein assemblies holds immense potential for various biotechnological applications. To address the...
In the ongoing quest for hybridizing discrete reasoning with neural nets, there is an increasing interest in neural architectures that can learn how to solve discrete reasoning or optimization problems from natural inputs. In this paper, we introduce a scalable neural architecture and loss function dedicated to learning the constraints and criteria...
In the ongoing quest for hybridizing discrete reasoning with neural nets, there is an increasing interest in neural architectures that can learn how to solve discrete reasoning or optimization problems from natural inputs. In this paper, we introduce a scalable neural architecture and loss function dedicated to learning the constraints and criteria...
To meet current societal demand for more sustainable transformation processes and bioresources, these processes must be optimized and new ones developed. The evolution of various systems (raw material, food, or process attributes) can be predicted to optimize the uses of biomass for better quality, safety, economic benefit, and sustainability. Pred...
N‐acetylglucosamine containing compounds acting as pathogenic or symbiotic signals are perceived by plant‐specific Lysin Motif Receptor‐Like Kinases (LysM‐RLKs). The molecular mechanisms of this perception are not fully understood, notably those of lipo‐chitooligosaccharides (LCOs) produced during root endosymbioses with nitrogen‐fixing bacteria or...
Miniprotein binders hold a great interest as a class of drugs that bridges the gap between monoclonal antibodies and small molecule drugs. Like monoclonal antibodies, they can be designed to bind to therapeutic targets with high affinity, but they are more stable and easier to produce and to administer. In this chapter, we present a structure-based...
Covalent protein complexes have been used to assemble enzymes in large scaffolds for biotechnology purposes. Although the catalytic mechanism of the covalent linking of such proteins is well known, the recognition and overall structural mechanisms driving the association are far less understood but could help further functional engineering of these...
Computational Protein Design (CPD) has produced impressive results for engineering new proteins, resulting in a wide variety of applications. In the past few years, various efforts have aimed at replacing or improving existing design methods using Deep Learning technology to leverage the amount of publicly available protein data. Deep Learning (DL)...
The development of protein and microorganism engineering have led to rising expectations of biotechnology in the design of emerging biomaterials, putatively of high interest to reduce our dependence on fossil carbon resources. In this way, cellulose, a renewable carbon based polysaccharide and derived products, displays unique properties used in ma...
Enzyme engineering approaches have allowed to extend the collection of enzymatic tools available for synthetic purposes. However, controlling the regioselectivity of the reaction remains challenging, in particular when dealing with carbohydrates bearing numerous reactive hydroxyl groups as substrates. Here, we used a computer-aided design framework...
Accurate DNA segregation is essential for faithful inheritance of genetic material. In bacteria, this process is mainly ensured by partition systems composed of two proteins, ParA and ParB, and a centromere site. Auto-regulation of Par operon expression is important for efficient partitioning and is primarily mediated by ParA for type Ia plasmid pa...
With the growing need for renewable sources of energy, the interest for enzymes capable of biomass degradation has been increasing. In this paper, we consider two different xylanases from the GH-11 family: the particularly active GH-11 xylanase from Neocallimastix patriciarum, NpXyn11A, and the hyper-thermostable mutant of the environmentally isola...
Proteins are the main active molecules of life. Although natural proteins play many roles, as enzymes or antibodies for example, there is a need to go beyond the repertoire of natural proteins to produce engineered proteins that precisely meet application requirements, in terms of function, stability, activity or other protein capacities. Computati...
Accurate DNA segregation is essential for faithful inheritance of genetic material. In bacteria, this process is mainly ensured by a partition system (Par) composed of two proteins, ParA and ParB, and a centromere site. The auto-regulation of Par operon expression is important for efficient partitioning, and is primarily mediated by ParA for type I...
Proteins are the main active molecules of Life. While natural proteins play many roles, as enzymes or antibodies for example, there is a need to go beyond the repertoire of natural proteins to produce engineered proteins that precisely meet application requirements, in terms of function, stability, activity or other protein capacities. Computationa...
The extant complex proteins must have evolved from ancient short and simple ancestors. Nevertheless, how such prototype proteins emerged on the primitive earth remains enigmatic. The double-psi beta-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reve...
Computational protein design (CPD) is a powerful technique for engineering new proteins, with both great fundamental implications and diverse practical interests. However, the approximations usually made for computational efficiency, using a single fixed backbone and a discrete set of side chain rotamers, tend to produce rigid and hyper-stable fold...
The use of retaining glycoside hydrolases as synthetic tools for glycochemistry is highly topical and the focus of considerable research. However, due to the incomplete identification of the molecular determinants of the transglycosylation/hydrolysis partition (t/h), rational engineering of retaining glycoside hydrolases to create transglycosylases...
Proteins are chains of simple molecules called amino acids. The sequence of amino acids in the chain defines the three-dimensional shape of the protein and ultimately its biochemical function. Over millions of years, living organisms have evolved a large catalog of proteins. By exploring the space of possible amino acid sequences, protein engineeri...
Enzymes are essential and ubiquitous biocatalysts involved in various metabolic pathways and used in many industrial processes. Here, we reframe enzymes not just as biocatalysts transforming bioproducts but also as sensitive probes for exploring the structure and composition of complex bioproducts, like meat tissue, dairy products and plant materia...
Present estimates suggest that of the 359 million tons of plastics produced annually worldwide¹, 150–200 million tons accumulate in landfill or in the natural environment². Poly(ethylene terephthalate) (PET) is the most abundant polyester plastic, with almost 70 million tons manufactured annually worldwide for use in textiles and packaging³. The ma...
Motivation:
Structure-based Computational Protein design (CPD) plays a critical role in advancing the field of protein engineering. Using an all-atom energy function, CPD tries to identify amino acid sequences that fold into a target structure and ultimately perform a desired function. The usual approach considers a single rigid backbone as a targ...
Structural motions are key events in enzyme catalysis, as exemplified by the conformational dynamics associated with the cofactor in the catalytic mechanism of hydrolytic NAD(P)-dependent aldehyde dehydrogenases. We previously showed that after the oxidoreduction step, the reduced cofactor must adopt a flipped conformation, which positions the nico...
Motivation:
Structure-based Computational Protein design (CPD) plays a critical role in advancing the field of protein engineering. Using an all-atom energy function, CPD tries to identify amino acid sequences that fold into a target structure and ultimately perform a desired function. Energy functions remain however imperfect and injecting releva...
Computational Protein Design (CPD) aims to predict amino acid sequences that fold to a specific structure and perform a desired function. CPD depends on a rotamer library, an energy function and an algorithm to search the sequence/conformation space. Variable Neighborhood Search (VNS) with Cost function networks is a powerful framework that can pro...
The present invention relates to mutant yeast strains, in particular mutant Yarrowia strains, capable of producing medium chain fatty acids compared to the parent oleaginous yeast strain from which said mutant oleaginous yeast strain derives. This invention also relates to means and methods for obtaining these mutant yeast strains.
The geometry and properties of the fitness landscapes of Computational Protein Design (CPD) are not well understood, due to the difficulty for sampling methods to access the NP-hard optima and explore their neighborhoods. In this paper, we enumerate all solutions within a 2 kcal/mol energy interval of the optimum of two CPD problems. We compute the...
Motivation:
Accurate and economic methods to predict change in protein binding free energy upon mutation are imperative to accelerate the design of proteins for a wide range of applications. Free energy is defined by enthalpic and entropic contributions. Following the recent progresses of Artificial Intelligence-based algorithms for guaranteed NP-...
The present invention relates to novel esterase, more particularly to esterase variants having improved thermostability compared to the esterase of SEQ ID N°1 and the uses thereof for degrading polyester containing material, such as plastic products. The esterases of the invention are particularly suited to degrade polyethylene terephthalate, and m...
The present invention relates to novel esterase, more particularly to esterase variants having improved activity compared to the esterase of SEQ ID N° 1 and the uses thereof for degrading polyester containing material, such as plastic products. The esterases of the invention are particularly suited to degrade polyethylene terephthalate, and materia...
Yarrowia lipolytica is a promising organism for the production of lipids of biotechnological interest and particularly for biofuel. In this study, we engineered the key enzyme involved in lipid biosynthesis, the giant multifunctional Fatty Acid Synthase (FAS), to shorten chain length of the synthesized fatty acids. Taking as starting point that the...
Amylosucrase from Neisseria polysaccharea naturally catalyzes the synthesis of α-1,4 glucans from sucrose. The product profile is quite polydisperse, ranging from soluble chains called maltooligosaccharides to high-molecular weight insoluble amylose. This enzyme was recently subjected to engineering of its active site to enable recognition of non-n...
Shortcomings in the definition of effective free energy surfaces of proteins are recognised to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD appl...
Significance
For many years, the development of adjuvants—compounds that boost the immunogenicity of vaccines—has been an empirical process. Adjuvants inducing a strong humoral immunity are available, but adjuvants directing the development of robust cellular immune responses are still needed. Recently, the C-type lectin receptor Mincle was found t...
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation mo...
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation mo...
A computer-aided engineering approach recently enabled to deeply reshape the active site of N. polysaccharea amylosucrase for recognition of non-natural acceptor substrates. Libraries of variants were constructed and screened on sucrose allowing the identification of 17 mutants able to synthesize molecules from sole sucrose, which are not synthesiz...
Computing the constant Z that normalizes an arbitrary distribution into a probability distribution is a difficult problem that has applications in statistics, biophysics and probabilistic reasoning. In biophysics, it is a prerequisite for the computation of the binding affinity between two molecules, a central question for protein design. In the ca...
Shortcomings in the definition of effective free energy surfaces of proteins are recognised to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD appl...
One of the main challenges in computational protein design (CPD) is the huge size of the protein sequence and conformational space that has to be computationally explored. Recently, we showed that state-of-the-art combinatorial optimization technologies based on Cost Function Network (CFN) processing allow speeding up provable rigid backbone protei...
Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD appl...
In Computational Protein Design (CPD), assuming a rigid backbone and amino-acid rotamer library, the problem of finding a sequence with an optimal conformation is NP-hard. In this paper, using Dunbrack's rotamer library and Talaris2014 decomposable energy function, we use an exact deterministic method combining branch and bound, arc consistency, an...
The exploration of chemo-enzymatic routes to complex carbohydrates has been hampered by the lack of appropriate enzymatic tools having the substrate specificity for new reactions. Here, we used a computer-aided design framework to guide the construction of a small, diversity-controlled library of amino acid sequences of an α-transglucosylase, the s...
Computational Protein Design aims at rationally designing amino-acid sequences that fold into a given three-dimensional structure and that will bestow the designed protein with desirable properties/functions. Usual criteria for design include stability of the designed protein and affinity between it and a ligand of interest. However, estimating the...
Amylosucrase from Neisseria polysaccharea is a remarkable transglucosylase that synthesizes an insoluble amylose-like polymer from sole substrate sucrose. One particular amino acid, Arg226, was proposed from molecular modeling studies to play an important role in the formation of the active site topology and in the accessibility of ligands to the c...
Proteins are chains of simple molecules called amino acids. The three-dimensional shape of a protein and its amino acid composition define its biological function. Over millions of years, living organisms have evolved a large catalog of proteins. By exploring the space of possible amino acid sequences, protein engineering aims at similarly designin...
Development of synthetic routes to complex carbohydrates and glyco-conjugates is often hampered by the lack of enzymes with requisite properties or specificities. Indeed, assembly or degradation of carbohydrates requires carbohydrate-active enzymes (CAZymes) able to act on a vast range of glycosidic monomers, oligomers or polymers in a regio-specif...
The main challenge for computational structure-based protein design (CPD) remains the combinatorial nature of the search space. Even in its simplest fixed-backbone formulation, CPD encompasses a computationally difficult NP-hard problem that prevents the exact exploration of complex systems defining large sequence-conformation spaces.
We present he...
Iterative saturation mutagenesis and combinatorial active site saturation focused on vicinal amino acids were used to alter the acceptor specificity of amylosucrase from Neisseria polysaccharea, a sucrose-utilizing α-transglucosidase, and sort out improved variants. From the screening of three semi-rational sub-libraries accounting in total for 20,...
Proteins are chains of simple molecules called amino acids. The three-dimensional shape of a protein and its amino acid composition define its biological function. Over millions of years, living organisms have evolved and produced a large catalog of proteins. By exploring the space of possible amino-acid sequences, protein engineering aims at simil...
This study is focused on the elucidation of the functional role of the mobile β2α2 loop in the α-l-arabinofuranosidase from Thermobacillus xylanilyticus, and particularly on the roles of loop residues H98 and W99. Using site-directed mutagenesis, coupled to characterization methods including isothermal titration calorimetry (ITC) and saturation tra...
Amylosucrases are sucrose-utilizing α-transglucosidases that naturally catalyze the synthesis of α-glucans, linked exclusively
through α1,4-linkages. Side products and in particular sucrose isomers such as turanose and trehalulose are also produced
by these enzymes. Here, we report the first structural and biophysical characterization of the most t...
This study is focused on the elucidation of the functional role of the mobile beta 2a2 loop in the a-l-arabinofuranosidase from Thermobacillus xylanilyticus, and particularly on the roles of loop residues H98 and W99. Using site-directed mutagenesis, coupled to characterization methods including isothermal titration calorimetry (ITC) and saturation...
Amylosucrases are sucrose-utilizing α-transglucosidases that naturally catalyze the synthesis of α-glucans, linked exclusively through α1,4-linkages. Side products and in particular sucrose isomers such as turanose and trehalulose are also produced by these enzymes. Here, we report the first structural and biophysical characterization of the most t...
AmpD is a cytoplasmic peptidoglycan (PG) amidase involved in bacterial cell-wall recycling and in induction of β-lactamase,
a key enzyme of β-lactam antibiotic resistance. AmpD belongs to the amidase_2 family that includes zinc-dependent amidases
and the peptidoglycan-recognition proteins (PGRPs), highly conserved pattern-recognition molecules of t...
Enantiomer discrimination by enzymes is a very accurate mechanism, which often involves few amino acids located at the active site. Lipase isoforms from Candida rugosa are very good enzymatic models to study this phenomenon as they display high sequence homology (>80%) and their enantioselectivity is often pointed out. In the present work, we inves...
Large-scale conformational rearrangement of a lid subdomain is a key event in the interfacial activation of many lipases. We present herein a study in which the large-scale "open-to-closed" movement of Burkholderia cepacia lipase lid has been simulated at the atomic level using a hybrid computational method. The two-stage approach combines path-pla...
AmpD is a cytoplasmic peptidoglycan (PG) amidase involved in bacterial cell-wall recycling and in induction of β-lactamase, a key enzyme of β-lactam antibiotic resistance. AmpD belongs to the amidase_2 family that includes zinc-dependent amidases and the peptidoglycan-recognition proteins (PGRPs), highly conserved pattern-recognition molecules of t...
This paper builds on the combination of robotic path planning algorithms and molecular modeling methods for computing large-amplitude molecular motions, and introduces voxel maps as a computational tool to encode and to represent such motions. We investigate several applications and show results that illustrate the interest of such representation.
We report the 1.7 Å resolution crystal structure of the Lip2 lipase from Yarrowia lipolytica in its closed conformation. The Lip2 structure is highly homologous to known structures of the fungal lipase family (Thermomyces lanuginosa, Rhizopus niveus, and Rhizomucor miehei lipases). However, it also presents some unique features that are described a...
The cover picture highlights the concept of adapting path-planning algorithms, originating from robotics, to investigating various molecular-motion problems, such as the access of R and S enantiomers to the active site of an enzyme. With this technique, both the enzyme and the substrates are modelled as polyarticulated mechanisms. On p. 2760 ff. of...
The interfacial activation of many lipases at water/lipid interface is mediated by large conformational changes of a so-called lid subdomain that covers up the enzyme active site. Here we investigated using molecular dynamic simulations in different explicit solvent environments (water, octane and water/octane interface) the molecular mechanism by...
Lipase from Burkholderia cepacia (BCL) has proven to be a very useful biocatalyst for the resolution of 2-substituted racemic acid derivatives, which are important chiral building blocks. Our previous work showed that enantioselectivity of the wild-type BCL could be improved by chemical engineering of the substrate's molecular structure. From this...
Understanding life at the atomic level requires the development of new methodologies, able to overcome the limitations of available experimental and computational techniques for the analysis of processes involving molecular motions. With this goal in mind, we develop new methods, combining robotic path planning algorithms and molecular modeling tec...
The sugar puckering of adenosine and uridine nucleosides with an amino group at 2' in the ribo or arabino orientations are determined using high-level quantum mechanical calculations Only the conformations that have dihedrals compatible with their insertion into a duplex are retained. The amino group has always been found to be pyramidal and its or...
A novel approach based on efficient path-planning algorithms was applied to investigate the influence of substrate access on Burkholderia cepacia lipase enantioselectivity. The system studied was the transesterification of 2-substituted racemic acid derivatives catalysed by B. cepacia lipase. In silico data provided by this approach showed a fair q...
We used high-level quantum mechanical calculations to determine the pucker (north type or south type) of various compounds: uridine, 2'-deoxyuridine, and 2'-O-methyl uridine. Although the dihedrals of the backbone are set close to their experimental values in double-stranded nucleic acids, calculations using density functional theory show that, in...
The HIV 1 integrase (IN) catalyses the insertion of the viral DNA into the infected cell's genome in two steps: the 3' processing and the strand transfer. We determined IN inhibitors binding mode (Styrylquinoline derivates) along the central domain' of the protein, in correlation with the proceeding mechanism found in vitro. To understand the effec...
The specific activity of the human immunodeficiency virus, type 1 (HIV-1), integrase on the viral long terminal repeat requires the binding of the enzyme to certain sequences located in the U3 and U5 regions at the ends of viral DNA, but the determinants of this specific DNA-protein recognition are not yet completely understood. We synthesized DNA...
Styrylquinoline derivatives (SQ) efficiently inhibit the 3'-processing activity of integrase (IN) with IC50 values of between 0.5 and 5 microM. We studied the mechanism of action of these compounds in vitro. First, we used steady-state fluorescence anisotropy to assay the effects of the SQ derivatives on the formation of IN-viral DNA complexes inde...
