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Xu H, Gao Q, Li L, Su T, Ming D. How alginate lyase produces quasi-monodisperse oligosaccharides: A normal-mode-based docking and molecular dynamics simulation study. Carbohydr Res 2024; 536:109022. [PMID: 38242069 DOI: 10.1016/j.carres.2024.109022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024]
Abstract
Oligosaccharide degradation products of alginate (AOS) hold significant potential in diverse fields, including pharmaceuticals, health foods, textiles, and agricultural production. Enzymatic alginate degradation is appealing due to its mild conditions, predictable activity, high yields, and controllability. However, the alginate degradation often results in a complex mixture of oligosaccharides, necessitating costly purification to isolate highly active oligosaccharides with a specific degree of polymerization (DP). Addressing this, our study centers on the alginate lyase AlyB from Vibrio Splendidus OU02, which uniquely breaks down alginate into mono-distributed trisaccharides. This enzyme features a polysaccharide lyase family 7 domain (PL-7) and a CBM32 carbohydrate-binding module connected by a helical structure. Through normal-mode-based docking and all-atom molecular simulations, we demonstrate that AlyB's substrate and product specificities are influenced by the spatial conformation of the catalytic pocket and the flexibility of its structure. The helically attached CBM is pivotal in releasing trisaccharides, which is crucial for avoiding further degradation. This study sheds light on AlyB's specificity and efficiency and contributes to the evolving field of enzyme design for producing targeted oligosaccharides, with significant implications for various bioindustries.
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Affiliation(s)
- Hengyue Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China; Now Studying in the State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Qi Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China
| | - Lu Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China
| | - Ting Su
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China
| | - Dengming Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China.
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Gao Q, Ming D. Protein-protein interactions enhance the thermal resilience of SpyRing-cyclized enzymes: A molecular dynamic simulation study. PLoS One 2022; 17:e0263792. [PMID: 35176056 PMCID: PMC8853484 DOI: 10.1371/journal.pone.0263792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/26/2022] [Indexed: 12/02/2022] Open
Abstract
Recently a technique based on the interaction between adhesion proteins extracted from Streptococcus pyogenes, known as SpyRing, has been widely used to improve the thermal resilience of enzymes, the assembly of biostructures, cancer cell recognition and other fields. It was believed that the covalent cyclization of protein skeleton caused by SpyRing reduces the conformational entropy of biological structure and improves its rigidity, thus improving the thermal resilience of the target enzyme. However, the effects of SpyTag/ SpyCatcher interaction with this enzyme are poorly understood, and their regulation of enzyme properties remains unclear. Here, for simplicity, we took the single domain enzyme lichenase from Bacillus subtilis 168 as an example, studied the interface interactions in the SpyRing by molecular dynamics simulations, and examined the effects of the changes of electrostatic interaction and van der Waals interaction on the thermal resilience of target enzyme. The simulations showed that the interface between SpyTag/SpyCatcher and the target enzyme is different from that found by geometric matching method and highlighted key mutations at the interface that might have effect on the thermal resilience of the enzyme. Our calculations highlighted interfacial interactions between enzyme and SpyTag/SpyCatcher, which might be useful in rational designs of the SpyRing.
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Affiliation(s)
- Qi Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing City, Jiangsu, PR China
| | - Dangling Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing City, Jiangsu, PR China
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Jiang J, Wang ZG. Improved local lattice Monte Carlo simulation for charged systems. J Chem Phys 2018; 148:114105. [DOI: 10.1063/1.5023491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jian Jiang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Zhen-Gang Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Chakravorty A, Jia Z, Li L, Alexov E. A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:2283-2295. [PMID: 28181811 PMCID: PMC9831612 DOI: 10.1021/acs.langmuir.6b04430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A new feature of the popular software DelPhi is developed and reported, allowing for computing the surface averaged electrostatic potential (SAEP) of macromolecules. The user is given the option to specify the distance from the van der Waals surface where the electrostatic potential will be outputted. In conjunction with DelPhiPKa and the BION server, the user can adjust the charges of titratable groups according to specific pH values, and add explicit ions bound to the macromolecular surface. This approach is applied to a set of four proteins with "experimentally" delivered zeta (ζ)-potentials at different pH values and salt concentrations. It has been demonstrated that the protocol is capable of predicting ζ-potentials in the case of proteins with relatively large net charges. This protocol has been less successful for proteins with low net charges. The work demonstrates that in the case of proteins with large net charges, the electrostatic potential should be collected at distances about 4 Å away from the vdW surface and explicit ions should be added at a binding energy cutoff larger than 1-2kT, in order to accurately predict ζ-potentials. The low salt conditions substantiate this effect of ions on SAEP.
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Affiliation(s)
- Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University , Clemson, South Carolina 29634, United States
| | - Zhe Jia
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University , Clemson, South Carolina 29634, United States
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University , Clemson, South Carolina 29634, United States
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University , Clemson, South Carolina 29634, United States
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Giese TJ, York DM. Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation. J Chem Theory Comput 2016; 12:2611-32. [PMID: 27171914 DOI: 10.1021/acs.jctc.6b00198] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed.
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Affiliation(s)
- Timothy J Giese
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8087, United States
| | - Darrin M York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8087, United States
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Xiao Y, Karttunen M, Jalkanen J, Mussi M, Liao Y, Grohe B, Lagugné-Labarthet F, Siqueira W. Hydroxyapatite Growth Inhibition Effect of Pellicle Statherin Peptides. J Dent Res 2015; 94:1106-12. [DOI: 10.1177/0022034515586769] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In our recent studies, we have shown that in vivo–acquired enamel pellicle is a sophisticated biological structure containing a significant portion of naturally occurring salivary peptides. From a functional aspect, the identification of peptides in the acquired enamel pellicle is of interest because many salivary proteins exhibit functional domains that maintain the activities of the native protein. Among the in vivo–acquired enamel pellicle peptides that have been newly identified, 5 peptides are derived from statherin. Here, we assessed the ability of these statherin pellicle peptides to inhibit hydroxyapatite crystal growth. In addition, atomistic molecular dynamics (MD) simulations were performed to better understand the underlying physical mechanisms of hydroxyapatite growth inhibition. A microplate colorimetric assay was used to quantify hydroxyapatite growth. Statherin protein, 5 statherin-derived peptides, and a peptide lacking phosphate at residues 2 and 3 were analyzed. Statherin peptide phosphorylated on residues 2 and 3 indicated a significant inhibitory effect when compared with the 5 other peptides ( P < 0.05). MD simulations showed a strong affinity and fast adsorption to hydroxyapatite for phosphopeptides, whereas unphosphorylated peptides interacted weakly with the hydroxyapatite. Our data suggest that the presence of a covalently linked phosphate group (at residues 2 and 3) in statherin peptides modulates the effect of hydroxyapatite growth inhibition. This study provides a mechanism to account for the composition and function of acquired enamel pellicle statherin peptides that will contribute as a base for the development of biologically stable and functional synthetic peptides for therapeutic use against dental caries and/or periodontal disease.
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Affiliation(s)
- Y. Xiao
- Schulich Dentistry and Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | - M. Karttunen
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - J. Jalkanen
- Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany
| | - M.C.M. Mussi
- Schulich Dentistry and Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | - Y. Liao
- Schulich Dentistry and Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | - B. Grohe
- Schulich Dentistry and Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | | | - W.L. Siqueira
- Schulich Dentistry and Department of Biochemistry, University of Western Ontario, London, ON, Canada
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