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Dhurua S, Jana M. Conformational preferences of heparan sulfate to recognize the CXCL8 dimer in aqueous medium: degree of sulfation and hydrogen bonds. Phys Chem Chem Phys 2024; 26:21888-21904. [PMID: 39105690 DOI: 10.1039/d4cp01430h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
The sulfation pattern and epimerization of the long-chain sulfated polysaccharide heparan sulfate (HS) cause structural diversity and regulate various physiological and pathological processes when binding with proteins. In this work, we performed a series of molecular dynamics simulations of three variants of the octadecasaccharide HS with varying sulfation positions in aqueous medium in their free forms and in the presence of the chemokine CXCL8 dimer. The free energy of binding depicts the sulfation at the 6-O position of GlcNAc (HS6S), and both 3-O and 6-O positions of GlcNAc (HS3S6S) of HS variants are more likely to bind with the CXCL8 dimer than the triply sulfated HS2S3S6S, which is sulfated at the 2-O position of GlcUA additionally along with 3-O and 6-O positions of GlcNAc. Binding between HS and CXCL8 was driven by electrostatic and van der Waals interactions predominantly regardless of the sulfation pattern; however, unfavorable entropic contribution suppressed the interaction between HS and CXCL8. The contribution of different amino acid residues to the binding energetics suggested that basic amino acids line up the binding site of CXCL8. This study further acknowledges the role of interfacial water that is structured and bound with HS through hydrogen bonds, exhibiting differential hydrogen bond relaxation dynamics compared to when the HS molecules are free. Moreover, this study identifies that with the increase in sulfation, the HS-water hydrogen bond relaxation occurs faster with the complexation, while the reverse trend is followed in their free forms. Significant structural adaptation of the different sulfated HS molecules, as verified from the free energy landscapes generated from various reaction coordinates, root-mean-square-deviations, end-to-end distances, including ring pucker angles, dihedral flexibility, and the high conformational entropy cost arising from the glycosidic bonds, suggests that the different sulfated variants of HS undergo significant structural transformation to bind with CXCL8. The presence of a CXCL8 dimer imposes the bound forms of HS to adopt non-linear structures with skew-boat conformations. The atomistic details of the study would help in understanding the selectivity and conformational diversity, as well as the role of solvents in the recognition of CXCL8 by different sulfated variants of HS molecules.
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Affiliation(s)
- Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela-769008, India.
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela-769008, India.
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Perera AS, Carlson CD, Cheramy J, Xu Y. Infrared and vibrational circular dichroism spectra of methyl β-D-glucopyranose in water: The application of the quantum cluster growth and clusters-in-a-liquid solvation models. Chirality 2023; 35:718-731. [PMID: 37162747 DOI: 10.1002/chir.23576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
The infrared (IR) and vibrational circular dichroism (VCD) spectra of methyl β-D-glucopyranose in water were measured. Both implicit and explicit solvation models were utilized to explain the observed spectra. The vast body of existing experimental and theoretical data suggested that about eight explicit water molecules are needed to account for the solvent effects, supported by the current Quantum Cluster Growth (QCG) analysis. Extensive manual and systematic conformational searches of the molecular target and its water clusters were carried out by using a recently developed conformational searching tool, conformer-rotamer ensemble sampling tool (CREST), and the microsolvation model in the associated QCG code. The Boltzmann averaged IR and VCD spectra of the methyl β-D-glucopyranose-(water)n (n = 8) conformers in the PCM of water provide better agreement with the experimental ones than those with n = 0, 1, and 2. The explicit solvation with eight water molecules was shown to greatly modify the conformational preference of methyl β-D-glucopyranose from its monomeric form. Further analyses show that the result is consistent with the existence of long-lived methyl β-D-glucopyranose monohydrates with the additional explicit water effects being accounted for with the quantum mechanical treatment of the other seven close-by water molecules in the PCM of water.
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Affiliation(s)
| | - Colton D Carlson
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Joseph Cheramy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Barros EP, Ries B, Champion C, Rieder SR, Riniker S. Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. J Chem Inf Model 2023; 63:1794-1805. [PMID: 36917685 PMCID: PMC10052353 DOI: 10.1021/acs.jcim.2c01610] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction, acting as more than just the surrounding medium by affecting the thermodynamics and thus the outcome of the binding process. As individual water contributions are impossible to measure experimentally, a range of computational methods have emerged to identify hydration sites in protein pockets and characterize their energetic contributions for drug discovery applications. Even though several methods model solvation effects explicitly, they focus on determining the stability of specific water sites independently and neglect solvation correlation effects upon replacement of clusters of water molecules, which typically happens in hit-to-lead optimization. In this work, we rigorously determine the conjoint effects of replacing all combinations of water molecules in protein binding pockets through the use of the RE-EDS multistate free-energy method, which combines Hamiltonian replica exchange (RE) and enveloping distribution sampling (EDS). Applications on the small bovine pancreatic trypsin inhibitor and four proteins of the bromodomain family illustrate the extent of solvation correlation effects on water thermodynamics, with the favorability of replacement of the water sites by pharmacophore probes highly dependent on the composition of the water network and the pocket environment. Given the ubiquity of water networks in biologically relevant protein targets, we believe our approach can be helpful for computer-aided drug discovery by providing a pocket-specific and a priori systematic consideration of solvation effects on ligand binding and selectivity.
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Affiliation(s)
- Emilia P Barros
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Benjamin Ries
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Candide Champion
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Salomé R Rieder
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Wei Y, Yu N, Zhu Y, Jia C, Xiao Y, Zhao Y, Cai P, Zhao W, Ju M, Wu T, Gan Z, Sun A. Characterization of blueberry (Vaccinium corymbosum L.) catechol oxidases III binding mechanism in response to selected substrates and inhibitors. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nance ML, Labonte JW, Adolf-Bryfogle J, Gray JJ. Development and Evaluation of GlycanDock: A Protein-Glycoligand Docking Refinement Algorithm in Rosetta. J Phys Chem B 2021; 125:10.1021/acs.jpcb.1c00910. [PMID: 34133179 PMCID: PMC8742512 DOI: 10.1021/acs.jpcb.1c00910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Carbohydrate chains are ubiquitous in the complex molecular processes of life. These highly diverse chains are recognized by a variety of protein receptors, enabling glycans to regulate many biological functions. High-resolution structures of protein-glycoligand complexes reveal the atomic details necessary to understand this level of molecular recognition and inform application-focused scientific and engineering pursuits. When experimental challenges hinder high-throughput determination of quality structures, computational tools can, in principle, fill the gap. In this work, we introduce GlycanDock, a residue-centric protein-glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. We performed a benchmark docking assessment using a set of 109 experimentally determined protein-glycoligand complexes as well as 62 unbound protein structures. The GlycanDock algorithm can sample and discriminate among protein-glycoligand models of native-like structural accuracy with statistical reliability from starting structures of up to 7 Å root-mean-square deviation in the glycoligand ring atoms. We show that GlycanDock-refined models qualitatively replicated the known binding specificity of a bacterial carbohydrate-binding module. Finally, we present a protein-glycoligand docking pipeline for generating putative protein-glycoligand complexes when only the glycoligand sequence and unbound protein structure are known. In combination with other carbohydrate modeling tools, the GlycanDock docking refinement algorithm will accelerate research in the glycosciences.
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Affiliation(s)
- Morgan L. Nance
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17603, United States
- Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania 17325, United States
| | - Jared Adolf-Bryfogle
- Protein Design Lab, Institute for Protein Innovation, Boston, Massachusetts 02115, United States
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jeffrey J. Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Chen Z, Lv Z, Sun Y, Chi Z, Qing G. Recent advancements in polyethyleneimine-based materials and their biomedical, biotechnology, and biomaterial applications. J Mater Chem B 2020; 8:2951-2973. [DOI: 10.1039/c9tb02271f] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Precise-synthesis strategies and integration approaches of bioinspired PEI-based systems, and their biomedical, biotechnology and biomaterial applications.
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Affiliation(s)
- Zhonghui Chen
- Guangdong Provincial Public Laboratory of Analysis and Testing Technology
- China National Analytical Center
- Guangzhou 510070
- China
- Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films
| | - Ziyu Lv
- Institute of Microscale Optoelectronics
- Shenzhen University
- Shenzhen 518000
- China
| | - Yifeng Sun
- Guangdong Provincial Public Laboratory of Analysis and Testing Technology
- China National Analytical Center
- Guangzhou 510070
- China
| | - Zhenguo Chi
- Guangdong Engineering Technology Research Center for High-performance Organic and Polymer Photoelectric Functional Films
- State Key Laboratory of OEMT
- School of Chemistry
- Sun Yat-sen University
- Guangzhou 510275
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116000
- China
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Passos da Silva D, Matwichuk ML, Townsend DO, Reichhardt C, Lamba D, Wozniak DJ, Parsek MR. The Pseudomonas aeruginosa lectin LecB binds to the exopolysaccharide Psl and stabilizes the biofilm matrix. Nat Commun 2019; 10:2183. [PMID: 31097723 PMCID: PMC6522473 DOI: 10.1038/s41467-019-10201-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/12/2019] [Indexed: 11/09/2022] Open
Abstract
Pseudomonas aeruginosa biofilms are composed of exopolysaccharides (EPS), exogenous DNA, and proteins that hold these communities together. P. aeruginosa produces lectins LecA and LecB, which possess affinities towards sugars found in matrix EPS and mediate adherence of P. aeruginosa to target host cells. Here, we demonstrate that LecB binds to Psl, a key matrix EPS, and this leads to increased retention of both cells and EPS in a growing biofilm. This interaction is predicted to occur between the lectin and the branched side chains present on Psl. Finally, we show that LecB coordinates Psl localization in the biofilm. This constitutes a unique function for LecB and identifies it as a matrix protein that contributes to biofilm structure through EPS interactions.
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Affiliation(s)
| | | | | | | | - Doriano Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Sede Secondaria di Basovizza, Trieste, Italy
| | - Daniel J Wozniak
- Departments of Microbial Infection and Immunity, Microbiology, Ohio State University, Columbus, OH, USA
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Integrative Microbiology Research Centre, South China Agricultural University, 510642, Guangzhou, China.
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