Catalytic Reaction Mechanism of Bacterial GH92 α‐1,2‐Mannosidase: A QM/MM Metadynamics Study DOI Creative Commons
Mert Sagiroglugil, Fatih Yaşar

ChemPhysChem, Journal Year: 2023, Volume and Issue: 24(24)

Published: Oct. 2, 2023

The catalytic mechanism of a Ca+2${C{a}^{+2}}$ -dependent family 92 α${{\rm \alpha }}$ -mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α-mannosidosis, has been investigated using quantum mechanics/molecular mechanics metadynamics methods. Computational efforts show that enzyme follows conformational itinerary ion serves dual purpose, as it not only distorts sugar ring but also plays crucial role orchestrating arrangement residues. This orchestration, turn, contributes facilitation OS2${{{\rm \ }}^{{\rm O}}{{\rm S}}_{2}}$ conformers for ensuing reaction. mechanistic insight well-aligned with experimental predictions pathway, computed energies are same order magnitude estimations. Hence, our results extend understanding glycosidases.

Language: Английский

Glycosyl Oxocarbenium Ions: Structure, Conformation, Reactivity, and Interactions DOI Creative Commons
Antonio Franconetti, Ana Ardá, Juan Luis Asensio

et al.

Accounts of Chemical Research, Journal Year: 2021, Volume and Issue: 54(11), P. 2552 - 2564

Published: April 30, 2021

ConspectusCarbohydrates (glycans, saccharides, and sugars) are essential molecules in all domains of life. Research on glycoscience spans from chemistry to biomedicine, including material science biotechnology. Access pure well-defined complex glycans using synthetic methods depends the success employed glycosylation reaction. In most cases, mechanism reaction is believed involve oxocarbenium ion. Understanding structure, conformation, reactivity, interactions this glycosyl cation predict outcome Account, building our contributions topic, we discuss theoretical experimental approaches that have been decipher key features cations, their structures reactivity.We also highlight that, a chemical perspective, can be described as continuum, unimolecular SN1 with naked cations intermediates bimolecular SN2-type mechanisms, which role counterions donors. All these factors should considered discussed herein. The importance dissociative mechanisms (involving contact ion pairs, solvent-separated solvent-equilibrated pairs) reactions highlighted.The calculations dynamics, reactivity discussed, highlighting advances field now allow access conformational preferences variety ions reactivities under SN1-like conditions.Specifically, ground-breaking use superacids generate emphasized, since it has permitted characterization structure conformation superacid solution by NMR spectroscopy.We pay special attention ions, conditions, counterions, possible intra- or intermolecular participation functional groups may stabilize nature acceptor, either weak strong nucleophile. We recent investigations different perspectives, identified involved ionic intermediates, estimating lifetimes studying other molecules. context, emphasize relationship between modulate sensitivity way modifying enzymes (glycosyl hydrolases transferases) build cleave glycosidic linkages nature. This comparison provides inspiration regulate stability cations.

Language: Английский

Citations

75
Multifaceted Computational Modeling in Glycoscience DOI
Serge Pérez, Olga Makshakova

Chemical Reviews, Journal Year: 2022, Volume and Issue: 122(20), P. 15914 - 15970

Published: July 5, 2022

Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates complex glycans. Such an ensemble involves one of most extensive sets quantity occurrence since they occur microorganisms higher organisms. Once compositions sequences these are established, determination their three-dimensional structural dynamical features is a step toward understanding molecular basis underlying properties functions. The range relevant computational methods capable addressing such issues anchored by specificity stereoelectronic effects from quantum chemistry to mesoscale modeling throughout dynamics mechanics coarse-grained docking calculations. Review leads reader through detailed presentations applications modeling. illustrations cover carbohydrate–carbohydrate interactions, glycolipids, N- O-linked glycans, emphasizing role SARS-CoV-2. presentation continues with structure polysaccharides solution solid-state lipopolysaccharides membranes. full protein-carbohydrate interactions presented, as exemplified carbohydrate-active enzymes, transporters, lectins, antibodies, glycosaminoglycan binding proteins. A final section list 150 tools databases help address many glycobioinformatics.

Language: Английский

Citations

53
Molecular simulations of complex carbohydrates and glycoconjugates DOI Creative Commons
Elisa Fadda

Current Opinion in Chemical Biology, Journal Year: 2022, Volume and Issue: 69, P. 102175 - 102175

Published: June 18, 2022

Complex carbohydrates (glycans) are the most abundant and versatile biopolymers in nature. The broad diversity of biochemical functions that cover is a direct consequence variety 3D architectures they can adopt, displaying branched or linear arrangements, widely ranging sizes, with highest building blocks any other natural biopolymer. Despite this unparalleled complexity, common denominator be found glycans' inherent flexibility, which hinders experimental characterization, but addressed by high-performance computing (HPC)-based molecular simulations. In short review, I present discuss state-of-the-art simulations complex glycoconjugates, highlighting methodological strengths weaknesses, important insights through emblematic case studies, suggesting perspectives for future developments.

Language: Английский

Citations

45
Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations DOI Creative Commons
M.A.B. Morais, Joan Coines, M.N. Domingues

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Jan. 14, 2021

Abstract Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, second most abundant carbohydrate plants. Here, we kinetically and mechanistically describe non-reducing-end xylose-releasing exo-oligoxylanase activity report crystal structure a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations active site xylosyl unit found, suggesting two alternative catalytic routes. These results confirmed by QM/MM simulations that unveil complete hydrolysis mechanism identify possible reaction pathways, involving different transition state for cleavage xylooligosaccharides. Such conformational promiscuity glycosidases is related open architecture thus might be extended other exo-acting enzymes. findings expand current general model glycosidases, main nature, impact on our understanding about their interaction substrates inhibitors.

Language: Английский

Citations

38
Glycosidase mechanisms: Sugar conformations and reactivity in endo- and exo-acting enzymes DOI Creative Commons
M.A.B. Morais, Alba Nin‐Hill, Carme Rovira

et al.

Current Opinion in Chemical Biology, Journal Year: 2023, Volume and Issue: 74, P. 102282 - 102282

Published: March 15, 2023

The enzymatic breakdown of carbohydrates plays a critical role in several biological events and enables the development sustainable processes to obtain bioproducts biofuels. In this scenario, design efficient inhibitors for glycosidases that can act as drug targets engineering carbohydrate-active enzymes with tailored catalytic properties is remarkable importance. To guide rational approaches, it necessary elucidate enzyme molecular mechanisms, particular understanding how microenvironment modulates conformational space explored by substrate. Computer simulations, especially those based on ab initio methods, have provided suitable atomic description carbohydrate conformations reactions glycosidase families. review, we will focus active-site topology (pocket or cleft) mode cleavage (endo exo) affect mechanisms adopted glycosidases, substrate along reaction coordinate.

Language: Английский

Citations

13
The Role of Sulfatides in Liver Health and Disease DOI Creative Commons
Chen Lin,

Montserrat Elizalde,

Gloria Álvarez‐Sola

et al.

Frontiers in Bioscience-Landmark, Journal Year: 2025, Volume and Issue: 30(1)

Published: Jan. 16, 2025

Sulfatides or 3-O-sulfogalactosylceramide are negatively charged sulfated glycosphingolipids abundant in the brain and kidneys play crucial roles nerve impulse conduction urinary pH regulation. present liver, specifically biliary tract. self-lipid antigens presented by cholangiocytes to activate cluster of differentiation 1d (CD1d)-restricted type II natural killer T (NKT) cells. These cells involved alcohol-related liver disease (ArLD) ischemic injury exert anti-inflammatory effects regulating activity pro-inflammatory I NKT Loss sulfatides has been implicated chronic inflammatory disorder known as primary sclerosing cholangitis (PSC); bile ducts deficient increase their permeability, resulting spread into parenchyma. Previous studies have shown elevated levels hepatocellular carcinoma (HCC), where could act adhesive molecules that contribute cancer metastasis. We recently demonstrated how loss function GAL3ST1, a limiting enzyme sulfatide synthesis, reduces tumorigenic capacity cholangiocarcinoma (CCA) The biological is still unclear; however, this review aims summarize existing findings on topic.

Language: Английский

Citations

0
Structure-Based Mechanism and Specificity of Human Galactosyltransferase β3GalT5 DOI Creative Commons
Jennifer M. Lo, Chih‐Chuan Kung, Ting-Jen Rachel Cheng

et al.

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: March 25, 2025

Human β1,3-galactosyltransferase 5 (β3GalT5) is a key enzyme involved in the synthesis of glycans on glycoproteins and glycolipids that are associated with various important biological functions, especially tumor malignancy cancer progression, has been considered as promising target for development anticancer agents. In this study, we determined X-ray structures β3GalT5 complex stable donor analogue UDP-2-fluorogalactose or native substrate UDP-galactose (UDP-Gal) several glycan acceptors at different reaction steps. Based obtained from our experiments, catalyzes transfer galactose UDP-Gal to broad spectrum an SN2-like mechanism; however, absence acceptor, slowly converted UDP two other products, one through mechanism water acceptor oxocarbenium-like product, presumably SN1-like mechanisms. The structure, mechanism, specificity presented study advance understanding enzymatic glycosylation provide valuable insights application drug design targeting β3GalT5-associated cancer.

Language: Английский

Citations

0
Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation DOI Creative Commons
Salila Pengthaisong, Beatriz Piniello, G.J. Davies

et al.

ACS Catalysis, Journal Year: 2023, Volume and Issue: 13(9), P. 5850 - 5863

Published: April 14, 2023

Retaining glycoside hydrolases use acid/base catalysis with an enzymatic protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile form covalent intermediate. Generally, this protonates laterally respect sugar ring, which places and carboxylates within about 4.5-6.5 Å of each other. However, in hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), distance between is around 8 (PDB: 5BVU) appears be above plane pyranose rather than being lateral that plane, could have consequences. no structure enzyme-substrate complex available for GH family. Here, we report structures Thermoanaerobacterium xylanolyticum (TxGH116) D593N mutant complexes cellobiose laminaribiose its mechanism. We confirm amide hydrogen bonding perpendicular orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations glycosylation half-reaction wild-type TxGH116 indicate substrate binds nonreducing glucose residue unusual relaxed 4C1 chair at -1 subsite. Nevertheless, reaction can still proceed through 4H3 half-chair transition state, as classical retaining β-glucosidases, D593 electron pair. The C6OH locked gauche, trans orientation C5-O5 C4-C5 bonds protonation. These data imply unique protonation trajectory Clan-O hydrolases, has strong implications design inhibitors specific either protonators, such GBA1, or GBA2.

Language: Английский

Citations

9
Late‐onset Krabbe disease presenting as spastic paraplegia – implications of GCase and CTSB/D DOI Creative Commons

Rebecca Mächtel,

Jan‐Philipp Dobert,

Ute Hehr

et al.

Annals of Clinical and Translational Neurology, Journal Year: 2024, Volume and Issue: 11(7), P. 1715 - 1731

Published: June 4, 2024

Krabbe disease (KD) is a multisystem neurodegenerative disorder with severe disability and premature death, mostly an infancy/childhood onset. In rare cases of late-onset phenotypes, symptoms are often milder difficult to diagnose. We here present translational approach combining diagnostic biochemical analyses male patient progressive gait starting at the age 44 years, final diagnosis KD (LOKD).

Language: Английский

Citations

3
Enzymatic Hydrolysis of Human Milk Oligosaccharides. The Molecular Mechanism of Bifidobacterium Bifidum Lacto-N-biosidase DOI Creative Commons
Irene Cuxart, Joan Coines, Oriol Esquivias

et al.

ACS Catalysis, Journal Year: 2022, Volume and Issue: 12(8), P. 4737 - 4743

Published: April 6, 2022

Bifidobacterium bifidum lacto-N-biosidase (LnbB) is a critical enzyme for the degradation of human milk oligosaccharides in gut microbiota breast-fed infants. Guided by recent crystal structures, we unveil its molecular mechanism catalysis using QM/MM metadynamics. We show that oligosaccharide substrate follows 1S3/1,4B → [4E]‡ 4C1/4H5 and [4E/4H5]‡ 1,4B conformational itineraries two successive reaction steps, with free energy barriers agreement experiments. The simulations also identify histidine (His263) switches between orientations to modulate pKa acid/base residue, facilitating catalysis. intermediate LnbB best depicted as an oxazolinium ion, minor population neutral oxazoline. present study sheds light on processing early life will be useful engineering similar glycosidases biocatalysis.

Language: Английский

Citations

13