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Prasher P, Sharma M, Agarwal V, Singh SK, Gupta G, Dureja H, Dua K. Cationic cycloamylose based nucleic acid nanocarriers. Chem Biol Interact 2024; 395:111000. [PMID: 38614318 DOI: 10.1016/j.cbi.2024.111000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/15/2024]
Abstract
Nucleic acid delivery by viral and non-viral methods has been a cornerstone for the contemporary gene therapy aimed at correcting the defective genes, replacing of the missing genes, or downregulating the expression of anomalous genes is highly desirable for the management of various diseases. Ostensibly, it becomes paramount for the delivery vectors to intersect the biological barriers for accessing their destined site within the cellular environment. However, the lipophilic nature of biological membranes and their potential to limit the entry of large sized, charged, hydrophilic molecules thus presenting a sizeable challenge for the cellular integration of negatively charged nucleic acids. Furthermore, the susceptibility of nucleic acids towards the degrading enzymes (nucleases) in the lysosomes present in cytoplasm is another matter of concern for their cellular and nuclear delivery. Hence, there is a pressing need for the identification and development of cationic delivery systems which encapsulate the cargo nucleic acids where the charge facilitates their cellular entry by evading the membrane barriers, and the encapsulation shields them from the enzymatic attack in cytoplasm. Cycloamylose bearing a closed loop conformation presents a robust candidature in this regard owing to its remarkable encapsulating tendency towards nucleic acids including siRNA, CpG DNA, and siRNA. The presence of numerous hydroxyl groups on the cycloamylose periphery provides sites for its chemical modification for the introduction of cationic groups, including spermine, (3-Chloro-2 hydroxypropyl) trimethylammonium chloride (Q188), and diethyl aminoethane (DEAE). The resulting cationic cycloamylose possesses a remarkable transfection efficiency and provides stability to cargo oligonucleotides against endonucleases, in addition to modulating the undesirable side effects such as unwanted immune stimulation. Cycloamylose is known to interact with the cell membranes where they release certain membrane components such as phospholipids and cholesterol thereby resulting in membrane destabilization and permeabilization. Furthermore, cycloamylose derivatives also serve as formulation excipients for improving the efficiency of other gene delivery systems. This review delves into the various vector and non-vector-based gene delivery systems, their advantages, and limitations, eventually leading to the identification of cycloamylose as an ideal candidate for nucleic acid delivery. The synthesis of cationic cycloamylose is briefly discussed in each section followed by its application for specific delivery/transfection of a particular nucleic acid.
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Affiliation(s)
- Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Energy Acres, Dehradun, 248007, India.
| | - Mousmee Sharma
- Department of Chemistry, Uttaranchal University, Dehradun, 248007, India
| | - Vipul Agarwal
- Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India; Faculty of Health, Australian Research Center in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia; School of Medical and Life Sciences, Sunway University, 47500 Sunway City, Malaysia
| | - Gaurav Gupta
- School of Pharmacy, Graphic Era Hill University, Dehradun, 248007, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharishi Dayanand University, Rohtak, 124001, India
| | - Kamal Dua
- Faculty of Health, Australian Research Center in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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2
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Liu JZ, Wang L, Jiang LJ, Lyu HC, Yuan Q, Wang GF, Fu YJ, Cui Q. In sight the behavior of natural Bletilla striata polysaccharide hydrocolloids by molecular dynamics method. Int J Biol Macromol 2024; 266:131245. [PMID: 38554922 DOI: 10.1016/j.ijbiomac.2024.131245] [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: 09/25/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Plant polysaccharides, distinguished by diverse glycosidic bonds and various cyclic sugar units, constitute a subclass of primary metabolites ubiquitously found in nature. Contrary to common understanding, plant polysaccharides typically form hydrocolloids upon dissolution in water, even though both excessively high and low temperatures impede this process. Bletilla striata polysaccharides (BSP), chosen for this kinetic study due to their regular repeating units, help elucidate the relationship between polysaccharide gelation and temperature. It is suggested that elevated temperatures enhance the mobility of BSP molecular chains, resulting in a notable acceleration of hydrogen bond breakage between BSP and water molecules and consequently, compromising the conformational stability of BSPs to some extent. This study unveils the unique relationship between polysaccharide dissolution processes and temperature from a kinetics perspective. Consequently, the conclusion provides a dynamical basis for comprehending the extraction and preparation of natural plant polysaccharide hydrocolloids, pharmaceuticals and related fields.
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Affiliation(s)
- Ju-Zhao Liu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, PR China.
| | - Lu Wang
- School of Life Sciences, Westlake University, Hangzhou 310030, PR China
| | - Li-Jie Jiang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| | - Hong-Chang Lyu
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Qiang Yuan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| | - Guang-Fu Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, PR China
| | - Yu-Jie Fu
- College of Forestry, Beijing Forestry University, No. 35, Tsinghua East Road, Haidian District, Beijing 100083, PR China
| | - Qi Cui
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, PR China.
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3
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Larsen D, Erichsen A, Masciotta G, Meier S, Beeren SR. Quantitative determination of the binding capabilities of individual large-ring cyclodextrins in complex mixtures. Chem Commun (Camb) 2024; 60:2090-2093. [PMID: 38294022 DOI: 10.1039/d3cc05897b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Large-ring cyclodextrins (CDs) are a comparatively unexplored family of macrocycles. We use high-resolution 1H-13C HSQC NMR experiments to resolve the anomeric signals of at least 13 different size CDs in a mixture. Using a single titration experiment, we can quantify the individual binding capabilites of these structurally-related hosts, avoiding the need for cumbersome isolation.
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Affiliation(s)
- Dennis Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
| | - Andreas Erichsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
| | - Giorgia Masciotta
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
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4
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Photenhauer AL, Villafuerte-Vega RC, Cerqueira FM, Armbruster KM, Mareček F, Chen T, Wawrzak Z, Hopkins JB, Vander Kooi CW, Janeček Š, Ruotolo BT, Koropatkin NM. The Ruminococcus bromii amylosome protein Sas6 binds single and double helical α-glucan structures in starch. Nat Struct Mol Biol 2024; 31:255-265. [PMID: 38177679 PMCID: PMC11081458 DOI: 10.1038/s41594-023-01166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 10/27/2023] [Indexed: 01/06/2024]
Abstract
Resistant starch is a prebiotic accessed by gut bacteria with specialized amylases and starch-binding proteins. The human gut symbiont Ruminococcus bromii expresses Sas6 (Starch Adherence System member 6), which consists of two starch-specific carbohydrate-binding modules from family 26 (RbCBM26) and family 74 (RbCBM74). Here, we present the crystal structures of Sas6 and of RbCBM74 bound with a double helical dimer of maltodecaose. The RbCBM74 starch-binding groove complements the double helical α-glucan geometry of amylopectin, suggesting that this module selects this feature in starch granules. Isothermal titration calorimetry and native mass spectrometry demonstrate that RbCBM74 recognizes longer single and double helical α-glucans, while RbCBM26 binds short maltooligosaccharides. Bioinformatic analysis supports the conservation of the amylopectin-targeting platform in CBM74s from resistant-starch degrading bacteria. Our results suggest that RbCBM74 and RbCBM26 within Sas6 recognize discrete aspects of the starch granule, providing molecular insight into how this structure is accommodated by gut bacteria.
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Affiliation(s)
- Amanda L Photenhauer
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Filipe M Cerqueira
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Krista M Armbruster
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tiantian Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, IL, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Craig W Vander Kooi
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Nicole M Koropatkin
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Auiewiriyanukul W, Saburi W, Ota T, Yu J, Kato K, Yao M, Mori H. Alteration of Substrate Specificity and Transglucosylation Activity of GH13_31 α-Glucosidase from Bacillus sp. AHU2216 through Site-Directed Mutagenesis of Asn258 on β→α Loop 5. Molecules 2023; 28:molecules28073109. [PMID: 37049872 PMCID: PMC10096246 DOI: 10.3390/molecules28073109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
α-Glucosidase catalyzes the hydrolysis of α-d-glucosides and transglucosylation. Bacillus sp. AHU2216 α-glucosidase (BspAG13_31A), belonging to the glycoside hydrolase family 13 subfamily 31, specifically cleaves α-(1→4)-glucosidic linkages and shows high disaccharide specificity. We showed previously that the maltose moiety of maltotriose (G3) and maltotetraose (G4), covering subsites +1 and +2 of BspAG13_31A, adopts a less stable conformation than the global minimum energy conformation. This unstable d-glucosyl conformation likely arises from steric hindrance by Asn258 on β→α loop 5 of the catalytic (β/α)8-barrel. In this study, Asn258 mutants of BspAG13_31A were enzymatically and structurally analyzed. N258G/P mutations significantly enhanced trisaccharide specificity. The N258P mutation also enhanced the activity toward sucrose and produced erlose from sucrose through transglucosylation. N258G showed a higher specificity to transglucosylation with p-nitrophenyl α-d-glucopyranoside and maltose than the wild type. E256Q/N258G and E258Q/N258P structures in complex with G3 revealed that the maltose moiety of G3 bound at subsites +1 and +2 adopted a relaxed conformation, whereas a less stable conformation was taken in E256Q. This structural difference suggests that stabilizing the G3 conformation enhances trisaccharide specificity. The E256Q/N258G-G3 complex formed an additional hydrogen bond between Met229 and the d-glucose residue of G3 in subsite +2, and this interaction may enhance transglucosylation.
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Affiliation(s)
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido Unifversity, Sapporo 060-8589, Japan; (W.A.)
- Correspondence: (W.S.); (H.M.); Tel.: +81-11-806-2508 (W.S.); +81-11-706-2497 (H.M.)
| | - Tomoya Ota
- Research Faculty of Agriculture, Hokkaido Unifversity, Sapporo 060-8589, Japan; (W.A.)
| | - Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido Unifversity, Sapporo 060-8589, Japan; (W.A.)
- Correspondence: (W.S.); (H.M.); Tel.: +81-11-806-2508 (W.S.); +81-11-706-2497 (H.M.)
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6
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Erichsen A, Peters GHJ, Beeren SR. Templated Enzymatic Synthesis of δ-Cyclodextrin. J Am Chem Soc 2023; 145:4882-4891. [PMID: 36802551 DOI: 10.1021/jacs.3c00341] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
While α-, β-, and γ-cyclodextrin (CD) are ubiquitous hosts employed by supramolecular chemists, δ-CD (formed from nine α-1,4-linked glucopyranose units) has received very little attention. α-, β-, and γ-CD are the major products of the enzymatic breakdown of starch by cyclodextrin glucanotransferase (CGTase), but δ-CD forms only transiently in this reaction, as a minor component of a complex mixture of linear and cyclic glucans. In this work, we show how δ-CD can be synthesized in unprecedented yields by employing a bolaamphiphile template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that δ-CD can thread up to three bolaamphiphiles forming [2]-, [3]-, or [4]-pseudorotaxanes, depending on the size of the hydrophilic headgroup and the length of the alkyl chain axle. Threading of the first bolaamphiphile occurs in fast exchange on the NMR chemical shift time scale, while subsequent threading occurs in slow exchange. To extract quantitative information for 1:2 and 1:3 binding events occurring in mixed exchange regimes, we derived equations for nonlinear curve fitting that take into consideration both the chemical shift changes for species in fast exchange and the integrals for species in slow exchange to determine Ka1, Ka2, and Ka3. Template T1 could be used to direct the enzymatic synthesis of δ-CD due to the cooperative formation of a 1:2 complex─the [3]-pseudorotaxane δ-CD·T12. Importantly, T1 is recyclable. It can be readily recovered from the enzymatic reaction by precipitation and reused in subsequent syntheses enabling preparative-scale synthesis of δ-CD.
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Affiliation(s)
- Andreas Erichsen
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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7
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Duran J. Role of Astrocytes in the Pathophysiology of Lafora Disease and Other Glycogen Storage Disorders. Cells 2023; 12:cells12050722. [PMID: 36899857 PMCID: PMC10000527 DOI: 10.3390/cells12050722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/05/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Lafora disease is a rare disorder caused by loss of function mutations in either the EPM2A or NHLRC1 gene. The initial symptoms of this condition are most commonly epileptic seizures, but the disease progresses rapidly with dementia, neuropsychiatric symptoms, and cognitive deterioration and has a fatal outcome within 5-10 years after onset. The hallmark of the disease is the accumulation of poorly branched glycogen in the form of aggregates known as Lafora bodies in the brain and other tissues. Several reports have demonstrated that the accumulation of this abnormal glycogen underlies all the pathologic traits of the disease. For decades, Lafora bodies were thought to accumulate exclusively in neurons. However, it was recently identified that most of these glycogen aggregates are present in astrocytes. Importantly, astrocytic Lafora bodies have been shown to contribute to pathology in Lafora disease. These results identify a primary role of astrocytes in the pathophysiology of Lafora disease and have important implications for other conditions in which glycogen abnormally accumulates in astrocytes, such as Adult Polyglucosan Body disease and the buildup of Corpora amylacea in aged brains.
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Affiliation(s)
- Jordi Duran
- Institut Químic de Sarrià (IQS), Universitat Ramon Llull (URL), 08017 Barcelona, Spain;
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
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8
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Baldassa MA, Dias RV, Oliveira LC, Feitosa E. Aqueous mixtures of cornstarch and Pluronic® F127 studied by experimental and computational techniques. Food Res Int 2022; 158:111515. [DOI: 10.1016/j.foodres.2022.111515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 11/30/2022]
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9
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Cerqueira FM, Photenhauer AL, Doden HL, Brown AN, Abdel-Hamid AM, Moraïs S, Bayer EA, Wawrzak Z, Cann I, Ridlon JM, Hopkins JB, Koropatkin NM. Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome. J Biol Chem 2022; 298:101896. [PMID: 35378131 PMCID: PMC9112005 DOI: 10.1016/j.jbc.2022.101896] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/08/2023] Open
Abstract
Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure-function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (Kd ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.
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Affiliation(s)
- Filipe M Cerqueira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Amanda L Photenhauer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Heidi L Doden
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Aric N Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ahmed M Abdel-Hamid
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Sarah Moraïs
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Edward A Bayer
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Zdzislaw Wawrzak
- Northwestern University, Synchrotron Research Center, Life Science Collaborative Access Team, Lemont, Illinois, USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jesse B Hopkins
- Biophysics Collaborative Access Team, Illinois Institute of Technology, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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Rho SJ, Kim YR. Improving solubility and stability of fat-soluble vitamins (A, D, E, and K) using large-ring cycloamylose. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Kabata D, Ryoki A, Kitamura S, Terao K. Chain Alignment of a Rigid Ring Polymer in the Lyotropic Liquid Crystal Phase: Cyclic Amylose Tris( n-butylcarbamate) in Tetrahydrofuran and Ethyl Lactate. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daigo Kabata
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Akiyuki Ryoki
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Shinichi Kitamura
- Center for Research and Development of Bioresources, Organization for Research Promotion, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai 599-8570, Japan
| | - Ken Terao
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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12
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Gavgani HN, Fawaz R, Ehyaei N, Walls D, Pawlowski K, Fulgos R, Park S, Assar Z, Ghanbarpour A, Geiger JH. A structural explanation for the mechanism and specificity of plant branching enzymes I and IIb. J Biol Chem 2021; 298:101395. [PMID: 34762912 PMCID: PMC8695356 DOI: 10.1016/j.jbc.2021.101395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/29/2022] Open
Abstract
Branching enzymes (BEs) are essential in the biosynthesis of starch and glycogen and play critical roles in determining the fine structure of these polymers. The substrates of these BEs are long carbohydrate chains that interact with these enzymes via multiple binding sites on the enzyme’s surface. By controlling the branched-chain length distribution, BEs can mediate the physiological properties of starch and glycogen moieties; however, the mechanism and structural determinants of this specificity remain mysterious. In this study, we identify a large dodecaose binding surface on rice BE I (BEI) that reaches from the outside of the active site to the active site of the enzyme. Mutagenesis activity assays confirm the importance of this binding site in enzyme catalysis, from which we conclude that it is likely the acceptor chain binding site. Comparison of the structures of BE from Cyanothece and BE1 from rice allowed us to model the location of the donor-binding site. We also identified two loops that likely interact with the donor chain and whose sequences diverge between plant BE1, which tends to transfer longer chains, and BEIIb, which transfers exclusively much shorter chains. When the sequences of these loops were swapped with the BEIIb sequence, rice BE1 also became a short-chain transferring enzyme, demonstrating the key role these loops play in specificity. Taken together, these results provide a more complete picture of the structure, selectivity, and activity of BEs.
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Affiliation(s)
- Hadi Nayebi Gavgani
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Remie Fawaz
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Nona Ehyaei
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - David Walls
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Kathryn Pawlowski
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Raoul Fulgos
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Sunghoon Park
- Department of Foodservice Management and Nutrition, College of Natural Sciences, Sangmyung University, Seoul, South Korea
| | - Zahra Assar
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - James H Geiger
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA.
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13
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Kerdpol K, Nutho B, Krusong K, Poo-arporn RP, Rungrotmongkol T, Hannongbua S. Encapsulation of α-tocopherol in large-ring cyclodextrin containing 26 α-D-glucopyranose units: A molecular dynamics study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Shao C, Feng Z, Westbrook JD, Peisach E, Berrisford J, Ikegawa Y, Kurisu G, Velankar S, Burley SK, Young JY. Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. Glycobiology 2021; 31:1204-1218. [PMID: 33978738 PMCID: PMC8457362 DOI: 10.1093/glycob/cwab039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/05/2021] [Accepted: 04/25/2021] [Indexed: 12/12/2022] Open
Abstract
Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable data representation for carbohydrates occurring in the PDB structures and the corresponding reference data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.
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Affiliation(s)
- Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Yasuyo Ikegawa
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, San Diego, CA 92093, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Y Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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15
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Urushibara K, Ferrand Y, Liu Z, Katagiri K, Kawahata M, Morvan E, D'Elia R, Pophristic V, Tanatani A, Huc I. Accessing Improbable Foldamer Shapes with Strained Macrocycles. Chemistry 2021; 27:11205-11215. [PMID: 33905165 PMCID: PMC8453500 DOI: 10.1002/chem.202101201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Indexed: 11/07/2022]
Abstract
The alkylation of some secondary amide functions with a dimethoxybenzyl (DMB) group in oligomers of 8-amino-2-quinolinecarboxylic acid destabilizes the otherwise favored helical conformations, and allows for cyclization to take place. A cyclic hexamer and a cyclic heptamer were produced in this manner. After DMB removal, X-ray crystallography and NMR show that the macrocycles adopt strained conformations that would be improbable in noncyclic species. The high helix folding propensity of the main chain is partly expressed in these conformations, but it remains frustrated by macrocyclization. Despite being homomeric, the macrocycles possess inequivalent monomer units. Experimental and computational studies highlight specific fluxional pathways within these structures. Extensive simulated annealing molecular dynamics allow for the prediction of the conformations for larger macrocycles with up to sixteen monomers.
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Affiliation(s)
- Ko Urushibara
- Department of ChemistryFaculty of ScienceOchanomizu University2-1-1 Otsuka, Bunkyo-kuTokyo112-8610Japan
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
| | - Yann Ferrand
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
| | - Zhiwei Liu
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Kosuke Katagiri
- Department of ChemistryFaculty of Science and EngineeringKonan University8-9-1 Okamoto, Higashinada-kuKobe658-8501Japan
| | - Masatoshi Kawahata
- Faculty of Pharmaceutical SciencesShowa Pharmaceutical University3-3165 Higashi-TamagawagakuenMachidaTokyo194-8543Japan
| | - Estelle Morvan
- IECB (UMS3033/US001)Université de Bordeaux, CNRS, INSERM2 rue Robert Escarpit33600PessacFrance
| | - Ryan D'Elia
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Vojislava Pophristic
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Aya Tanatani
- Department of ChemistryFaculty of ScienceOchanomizu University2-1-1 Otsuka, Bunkyo-kuTokyo112-8610Japan
| | - Ivan Huc
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
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16
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Solubility enhancement of poorly water soluble domperidone by complexation with the large ring cyclodextrin. Int J Pharm 2021; 606:120909. [PMID: 34298103 DOI: 10.1016/j.ijpharm.2021.120909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/10/2021] [Accepted: 07/18/2021] [Indexed: 12/25/2022]
Abstract
The water solubility of domperidone (DMP) could be improved by complexation with large ring cyclodextrins (LR-CDs). LR-CDs contain a relatively hydrophobic cavity that is capable of entrapping the molecules to form inclusion complexes. The complex formation capability of mixture LR-CDs having a degree of polymerization (DP) of 22-48, with DMP was investigated. The phase solubility profile of mixture LR-CD/DMP was classified as AN-type, resulting in increased DMP solubility in water by 3-fold. Various physicochemical techniques confirmed the mixture LR-CD/DMP complex formation. Single LR-CD with DP of 26, 27, 28, 29, 30, 33 and 34 (CD26 ~ CD34) were isolated from LR-CD mixtures using ODS column for HPLC separation. The CD33/DMP complex has demonstrated the most significant improvement compared to other single LR-CD complexes with a 2.7-fold increase in DMP solubility. The molecular dynamic result revealed that DMP formed stable complexes with CD33 by positioned fully encapsulated inside the cavity and covered by 13-14 subunits of CD33.
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18
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Khatami MH, Barber W, de Haan HW. Using geometric criteria to study helix-like structures produced in molecular dynamics simulations of single amylose chains in water. RSC Adv 2021; 11:11992-12002. [PMID: 35423775 PMCID: PMC8697119 DOI: 10.1039/d1ra00071c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/02/2021] [Indexed: 11/25/2022] Open
Abstract
Amylose is a linear polymer chain of α-d-glucose units connected through α(1 → 4) glycosidic bonds. Experimental studies show that in non-polar solvents, single amylose chains form helical structures containing precise H-bond patterns. However, both experimental and computational studies indicate that these perfectly H-bonded helices are not stable in pure water. Nevertheless, amylose chains are observed to form helix-like structures in molecular dynamics (MD) simulations that exhibit imperfect H-bond patterns. In this paper, we study the structure of amylose chains in water using MD simulations to identify and characterize these “imperfect” helical structures. To this end we devise geometry-based criteria to define imperfect helical structures in amylose chains. Using this approach, the propensity of amylose chains to form these structures is quantified as a function of chain length and solvent temperature. This analysis also uncovers both short and long time helix-breaking mechanisms such as band-flips and kinks in the chain. This geometric approach to defining imperfect helices thus allows us to give new insight into the secondary structure of single amylose chains in spite of imperfect H-bond patterns. We introduce a geometrical approach to capture and study helix-like structures in MD simulations of single amylose chains in water.![]()
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Affiliation(s)
| | - William Barber
- Ontario Tech University, Department of Physics 2000 Simcoe St N Oshawa ON L1H 7K4. Canada
| | - Hendrick W de Haan
- Ontario Tech University, Department of Physics 2000 Simcoe St N Oshawa ON L1H 7K4. Canada
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19
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20
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Mishra KA, Adamson J, Öeren M, Kaabel S, Fomitšenko M, Aav R. Dynamic chiral cyclohexanohemicucurbit[12]uril. Chem Commun (Camb) 2020; 56:14645-14648. [PMID: 33155596 DOI: 10.1039/d0cc06817a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy and DFT modeling studies of chiral cyclohexanohemicucurbit[12]uril indicate that the macrocycle adopts a concave octagonal shape with two distinct conformational flexibilities in solution. Methylene bridge flipping occurs at temperatures above 265 K, while urea monomers rotate at temperatures above 308 K, resulting in the loss of confined space within the macrocycle.
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Affiliation(s)
- Kamini A Mishra
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Jasper Adamson
- Chemical Physics Laboratory, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Mario Öeren
- Optibrium Limited, F5-6 Blenheim House, Denny End Road, Cambridge, CB25 9PB, UK
| | - Sandra Kaabel
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia. and Department of Chemistry, McGill University, 801 Sherbrooke Street West, H3A 0B8, Montreal, Quebec, Canada
| | - Maria Fomitšenko
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Riina Aav
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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21
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Size and shape of cycloamylose estimated using column chromatography coupled with small-angle X-ray scattering. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.105948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Imamura K, Matsuura T, Nakagawa A, Kitamura S, Kusunoki M, Takaha T, Unno H. Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato. Protein Sci 2020; 29:2085-2100. [PMID: 32808707 PMCID: PMC7513719 DOI: 10.1002/pro.3932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 11/06/2022]
Abstract
Starch produced by plants is a stored form of energy and is an important dietary source of calories for humans and domestic animals. Disproportionating enzyme (D-enzyme) catalyzes intramolecular and intermolecular transglycosylation reactions of α-1, 4-glucan. D-enzyme is essential in starch metabolism in the potato. We present the crystal structures of potato D-enzyme, including two different types of complex structures: a primary Michaelis complex (substrate binding mode) for 26-meric cycloamylose (CA26) and a covalent intermediate for acarbose. Our study revealed that the acarbose and CA26 reactions catalyzed by potato D-enzyme involve the formation of a covalent intermediate with the donor substrate. HPAEC of reaction substrates and products revealed the activity of the potato D-enzyme on acarbose and CA26 as donor substrates. The structural and chromatography analyses provide insight into the mechanism of the coupling reaction of CA and glucose catalyzed by the potato D-enzyme. The enzymatic reaction mechanism does not involve residual hydrolysis. This could be particularly useful in preventing unnecessary starch degradation leading to reduced crop productivity. Optimization of this mechanism would be important for improvements of starch storage and productivity in crops.
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Affiliation(s)
- Kayo Imamura
- Laboratory of Enzyme Chemistry, Graduate School of Agriculture and Biological ScienceOsaka Prefecture UniversityOsakaJapan
| | | | | | - Shinichi Kitamura
- Laboratory of Biophysical Chemistry, Graduate School of Agriculture and Biological ScienceOsaka Prefecture UniversityOsakaJapan
- Present address:
Laboratory of Advanced Food Process EngineeringOsaka Prefecture University, 1‐2, Gakuen‐cho, Nakaku, Osaka, Sakai 599‐8570Japan
| | | | - Takeshi Takaha
- Biochemical Research LaboratoriesEzaki Glico Co., LtdOsakaJapan
- Present address:
Sanawa Starch Co., Ltd. 594 Unate, Kashihara, Nara 634‐8585Japan
| | - Hideaki Unno
- Graduate School of EngineeringNagasaki UniversityNagasakiJapan
- Organization for Marine Science and TechnologyNagasaki UniversityNagasakiJapan
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23
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Zhou Y, van Zijl PCM, Xu J, Yadav NN. Mechanism and quantitative assessment of saturation transfer for water-based detection of the aliphatic protons in carbohydrate polymers. Magn Reson Med 2020; 85:1643-1654. [PMID: 32970889 DOI: 10.1002/mrm.28503] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE CEST MRI experiments of mobile macromolecules, for example, proteins, carbohydrates, and phospholipids, often show signals due to saturation transfer from aliphatic protons to water. Currently, the mechanism of this nuclear Overhauser effect (NOE)-based transfer pathway is not completely understood and could be due either to NOEs directly to bound water or NOEs relayed intramolecularly via exchangeable protons. We used glycogen as a model system to investigate this saturation transfer pathway in sugar polymer solution. METHODS To determine whether proton exchange affected saturation transfer, saturation spectra (Z-spectra) were measured for glycogen solutions of different pH, D2 O/H2 O ratio, and glycogen particle size. A theoretical model was derived to analytically describe the NOE-based signals in these spectra. Numerical simulations were performed to verify this theory, which was further tested by fitting experimental data for different exchange regimes. RESULTS Signal intensities of aliphatic NOEs in Z-spectra of glycogen in D2 O solution were influenced by hydroxyl proton exchange rates, whereas those in H2 O were not. This indicates that the primary transfer pathway is an exchange-relayed NOE from these aliphatic protons to neighboring hydroxyl protons, followed by the exchange to water protons. Experimental data for glycogen solutions in D2 O and H2 O could be analyzed successfully using an analytical theory derived for such relayed NOE transfer, which was further validated using numerical simulations with the Bloch equations. CONCLUSION The predominant mechanism underlying aliphatic signals in Z-spectra of mobile carbohydrate polymers is intramolecular relayed NOE transfer followed by proton exchange.
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Affiliation(s)
- Yang Zhou
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Peter C M van Zijl
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Jiadi Xu
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Nirbhay N Yadav
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
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24
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Jung YK, Joo KS, Rho SJ, Kim YR. pH-dependent antioxidant stability of black rice anthocyanin complexed with cycloamylose. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109474] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Schahl A, Réat V, Jolibois F. Structures and NMR spectra of short amylose-lipid complexes. Insight using molecular dynamics and DFT quantum chemical calculations. Carbohydr Polym 2020; 235:115846. [DOI: 10.1016/j.carbpol.2020.115846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/06/2019] [Accepted: 01/08/2020] [Indexed: 01/29/2023]
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26
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Meng Y, Lyu F, Xu X, Zhang L. Recent Advances in Chain Conformation and Bioactivities of Triple-Helix Polysaccharides. Biomacromolecules 2020; 21:1653-1677. [PMID: 31986015 DOI: 10.1021/acs.biomac.9b01644] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural polysaccharides derived from renewable biomass sources are regarded as environmentally friendly and sustainable polymers. As the third most abundant biomacromolecule in nature, after proteins and nucleic acids, polysaccharides are also closely related with many different life activities. In particular, β-glucans are one of the most widely reported bioactive polysaccharides and are usually considered as biological response modifiers. Among them, β-glucans with triple-helix conformation have been the hottest and most well-researched polysaccharides at present, especially lentinan and schizophyllan, which are clinically used as cancer therapies in some Asian countries. Thus, creation of these active triple-helix polysaccharides is beneficial to the research and development of sustainable "green" biopolymers in the fields of food and life sciences. Therefore, full fundamental research of triple-helix polysaccharides is essential to discover more applications for polysaccharides. In this Review, the recent research progress of chain conformations, bioactivities, and structure-function relationships of triple-helix β-glucans is summarized. The main contents include the characterization methods of the macromolecular conformation, proof of triple helices, bioactivities, and structure-function relationships. We believe that the governments, enterprises, universities, and institutes dealing with the survival and health of human beings can expect the development of natural bioproducts in the future. Hence, a deep understanding of β-glucans with triple-helix chain conformation is necessary for application of natural medicines and biologics for a sustainable world.
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Affiliation(s)
- Yan Meng
- College of Chemistry & Molecule Sciences, Wuhan University, Wuhan 430072, China.,College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Fengzhi Lyu
- College of Chemistry & Molecule Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaojuan Xu
- College of Chemistry & Molecule Sciences, Wuhan University, Wuhan 430072, China
| | - Lina Zhang
- College of Chemistry & Molecule Sciences, Wuhan University, Wuhan 430072, China
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27
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Park J, Rho SJ, Kim YR. Enhancing antioxidant and antimicrobial activity of carnosic acid in rosemary (Rosmarinus officinalis L.) extract by complexation with cyclic glucans. Food Chem 2019; 299:125119. [DOI: 10.1016/j.foodchem.2019.125119] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 11/15/2022]
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28
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Modification of cereal and tuber waxy starches with radio frequency cold plasma and its effects on waxy starch properties. Carbohydr Polym 2019; 223:115075. [DOI: 10.1016/j.carbpol.2019.115075] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022]
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29
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Kim D, Ryoki A, Kabata D, Kitamura S, Terao K. Lyotropic Liquid Crystallinity of Linear and Cyclic Amylose Derivatives: Amylose Tris( n-octadecylcarbamate) in Tetrahydrofuran and 2-Octanone. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- DongChan Kim
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Akiyuki Ryoki
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Daigo Kabata
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shinichi Kitamura
- Center for Research and Development of Bioresources, Organization for Research Promotion, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai 599-8570, Japan
| | - Ken Terao
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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30
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Exploring and Exploiting the Symmetry-Breaking Effect of Cyclodextrins in Mechanomolecules. Symmetry (Basel) 2019. [DOI: 10.3390/sym11101249] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cyclodextrins (CDs) are cone-shaped molecular rings that have been widely employed in supramolecular/host–guest chemistry because of their low cost, high biocompatibility, stability, wide availability in multiple sizes, and their promiscuity for binding a range of molecular guests in water. Consequently, CD-based host–guest complexes are often employed as templates for the synthesis of mechanically bonded molecules (mechanomolecules) such as catenanes, rotaxanes, and polyrotaxanes in particular. The conical shape and cyclodirectionality of the CD “bead” gives rise to a symmetry-breaking effect when it is threaded onto a molecular “string”; even symmetrical guests are rendered asymmetric by the presence of an encircling CD host. This review focuses on the stereochemical implications of this symmetry-breaking effect in mechanomolecules, including orientational isomerism, mechanically planar chirality, and topological chirality, as well as how they support applications in regioselective and stereoselective chemical synthesis, the design of molecular machine prototypes, and the development of advanced materials.
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31
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Koneru JK, Zhu X, Mondal J. Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields. J Chem Theory Comput 2019; 15:6203-6212. [DOI: 10.1021/acs.jctc.9b00630] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jaya Krishna Koneru
- Tata Institute of Fundamental Research, Centre For Interdisciplinary Sciences, Hyderabad 500107, India
| | - Xiao Zhu
- Department of Agricultural and Biological Engineering, Research Computing, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Centre For Interdisciplinary Sciences, Hyderabad 500107, India
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32
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Larsen D, Beeren SR. Enzyme-mediated dynamic combinatorial chemistry allows out-of-equilibrium template-directed synthesis of macrocyclic oligosaccharides. Chem Sci 2019; 10:9981-9987. [PMID: 32055354 PMCID: PMC6979337 DOI: 10.1039/c9sc03983j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/02/2019] [Indexed: 12/16/2022] Open
Abstract
Artificial templates can control out-of-equilibrium self-assembly in an enzyme-mediated dynamic system of cyclodextrins, even allowing access to products not selected in Nature.
We show that the outcome of enzymatic reactions can be manipulated and controlled by using artificial template molecules to direct the self-assembly of specific products in an enzyme-mediated dynamic system. Specifically, we utilize a glycosyltransferase to generate a complex dynamic mixture of interconverting linear and macrocyclic α-1,4-d-glucans (cyclodextrins). We find that the native cyclodextrins (α, β and γ) are formed out-of-equilibrium as part of a kinetically trapped subsystem, that surprisingly operates transiently like a Dynamic Combinatorial Library (DCL) under thermodynamic control. By addition of different templates, we can promote the synthesis of each of the native cyclodextrins with 89–99% selectivity, or alternatively, we can amplify the synthesis of unusual large-ring cyclodextrins (δ and ε) with 9 and 10 glucose units per macrocycle. In the absence of templates, the transient DCL lasts less than a day, and cyclodextrins convert rapidly to short maltooligosaccharides. Templates stabilize the kinetically trapped subsystem enabling robust selective synthesis of cyclodextrins, as demonstrated by the high-yielding sequential interconversion of cyclodextrins in a single reaction vessel. Our results show that given the right balance between thermodynamic and kinetic control, templates can direct out-of-equilibrium self-assembly, and be used to manipulate enzymatic transformations to favor specific and/or alternative products to those selected in Nature.
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Affiliation(s)
- Dennis Larsen
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , DK-2800 Kongens Lyngby , Denmark .
| | - Sophie R Beeren
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , DK-2800 Kongens Lyngby , Denmark .
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33
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Lv R, Qi L, Zou Y, Zou J, Luo Z, Shao P, Tamer TM. Preparation and structural properties of amylose complexes with quercetin and their preliminary evaluation in delivery application. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2019. [DOI: 10.1080/10942912.2019.1651736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rui Lv
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Liang Qi
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Yuxiao Zou
- Sericultural & Agri-Food Research Institute GAAS, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jinfeng Zou
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Zhigang Luo
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- South China Institute of Collaborative Innovation, Dongguan, China
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| | - Ping Shao
- Department of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Tamer Mahmoud Tamer
- Polymer Materials Research Department, Advanced Technology and New Materials Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Egypt
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Khatun A, Waters DLE, Liu L. A Review of Rice Starch Digestibility: Effect of Composition and Heat‐Moisture Processing. STARCH-STARKE 2019. [DOI: 10.1002/star.201900090] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Amina Khatun
- Southern Cross Plant Science, Southern Cross UniversityLismoreNSW2480Australia
| | - Daniel L. E. Waters
- Southern Cross Plant Science, Southern Cross UniversityLismoreNSW2480Australia
- ARC ITTC for Functional Grains, Charles Sturt UniversityWagga WaggaNSW2650Australia
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross UniversityLismoreNSW2480Australia
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Lemos PVF, Barbosa LS, Ramos IG, Coelho RE, Druzian JI. Characterization of amylose and amylopectin fractions separated from potato, banana, corn, and cassava starches. Int J Biol Macromol 2019; 132:32-42. [PMID: 30880053 DOI: 10.1016/j.ijbiomac.2019.03.086] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 10/27/2022]
Abstract
Analytical techniques such HPSEC, DSC, and TGA have been employed for amylose determination in starch samples, though spectrophotometry by iodine binding is most commonly used. The vast majority of these techniques require an analytical curve, using amylose and amylopectin standards with physicochemical properties similar to those found in the original starch. The current study aimed to obtain the amylose and amylopectin fractions from potato, banana, corn, and cassava starches, characterize them, and evaluate their behavior via thermogravimetric curves. Blue amylose iodine complex and HPSEC-DRI methods have obtained high purity amylose and amylopectin fractions. All molecular weights of the obtained amylose and amylopectin fractions were similar to those presented in other reports. Different results were obtained by deconvolution of the amylopectin polymodal distribution. All amyloses presented as semi-crystalline V-type polymorphs, while all amylopectin fractions were amorphous. The Tg of all Vamyloses presented were directly proportional to their respective crystalline index. TGA evaluations have shown that selective precipitation of amylose with 1-butanol strongly changes its thermal behavior. Therefore, the separation procedure used was an ineffective pathway for obtaining standards for thermal studies.
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Affiliation(s)
- Paulo Vitor França Lemos
- Faculty of Pharmacy, Federal University of Bahia, Rua Barão de Jeremoabo, 147, Campus Universitário de Ondina, 40. 170-115, Salvador, BA, Brazil.
| | - Leandro Santos Barbosa
- Faculty of Pharmacy, Federal University of Bahia, Rua Barão de Jeremoabo, 147, Campus Universitário de Ondina, 40. 170-115, Salvador, BA, Brazil
| | - Ingrid Graça Ramos
- Faculty of Pharmacy, Federal University of Bahia, Rua Barão de Jeremoabo, 147, Campus Universitário de Ondina, 40. 170-115, Salvador, BA, Brazil
| | | | - Janice Izabel Druzian
- Faculty of Pharmacy, Federal University of Bahia, Rua Barão de Jeremoabo, 147, Campus Universitário de Ondina, 40. 170-115, Salvador, BA, Brazil.
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36
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Pendrill R, Mutter ST, Mensch C, Barron LD, Blanch EW, Popelier PLA, Widmalm G, Johannessen C. Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity. Chemphyschem 2019; 20:695-705. [PMID: 30688397 DOI: 10.1002/cphc.201801172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/25/2019] [Indexed: 01/31/2023]
Abstract
Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.
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Affiliation(s)
- Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
| | - Shaun T Mutter
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Natural Sciences, Middlesex University, NW4 4BT, London, UK
| | - Carl Mensch
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Ghent Quantum Chemistry Group Department of Chemistry, University of Ghent, Krijgslaan 281, 9000, Ghent, Belgium
| | - Laurence D Barron
- School of Chemistry, University of Glasgow Joseph Black Building, Glasgow, G12 8QQ, UK
| | - Ewan W Blanch
- School of Science, RMIT University GPO Box 2476, Melbourne, VIC 3001, Australia
| | - Paul L A Popelier
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
| | - Christian Johannessen
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171, 2020, Antwerp, Belgium
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Brewer MK, Gentry MS. Brain Glycogen Structure and Its Associated Proteins: Past, Present and Future. ADVANCES IN NEUROBIOLOGY 2019; 23:17-81. [PMID: 31667805 PMCID: PMC7239500 DOI: 10.1007/978-3-030-27480-1_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This chapter reviews the history of glycogen-related research and discusses in detail the structure, regulation, chemical properties and subcellular distribution of glycogen and its associated proteins, with particular focus on these aspects in brain tissue.
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Affiliation(s)
- M Kathryn Brewer
- Department of Molecular and Cellular Biochemistry, Epilepsy and Brain Metabolism Center, Lafora Epilepsy Cure Initiative, and Center for Structural Biology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, Epilepsy and Brain Metabolism Center, Lafora Epilepsy Cure Initiative, and Center for Structural Biology, University of Kentucky College of Medicine, Lexington, KY, USA.
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38
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Miao M, Jiang B, Jin Z, BeMiller JN. Microbial Starch-Converting Enzymes: Recent Insights and Perspectives. Compr Rev Food Sci Food Saf 2018; 17:1238-1260. [PMID: 33350152 DOI: 10.1111/1541-4337.12381] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Ming Miao
- State Key Laboratory of Food Science & Technology; Jiangnan Univ.; 1800 Lihu Ave. Wuxi Jiangsu 214122 P. R. China
| | - Bo Jiang
- State Key Laboratory of Food Science & Technology; Jiangnan Univ.; 1800 Lihu Ave. Wuxi Jiangsu 214122 P. R. China
| | - Zhengyu Jin
- State Key Laboratory of Food Science & Technology; Jiangnan Univ.; 1800 Lihu Ave. Wuxi Jiangsu 214122 P. R. China
| | - James N. BeMiller
- State Key Laboratory of Food Science & Technology; Jiangnan Univ.; 1800 Lihu Ave. Wuxi Jiangsu 214122 P. R. China
- Dept. of Food Science; Whistler Center for Carbohydrate Research, Purdue Univ.; 745 Agriculture Mall Drive West Lafayette IN 47907-2009 U.S.A
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39
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Auiewiriyanukul W, Saburi W, Kato K, Yao M, Mori H. Function and structure of GH13_31 α-glucosidase with high α-(1→4)-glucosidic linkage specificity and transglucosylation activity. FEBS Lett 2018; 592:2268-2281. [PMID: 29870070 DOI: 10.1002/1873-3468.13126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/11/2018] [Accepted: 05/22/2018] [Indexed: 11/12/2022]
Abstract
α-Glucosidase hydrolyzes α-glucosides and transfers α-glucosyl residues to an acceptor through transglucosylation. In this study, GH13_31 α-glucosidase BspAG13_31A with high transglucosylation activity is reported in Bacillus sp. AHU2216 and biochemically and structurally characterized. This enzyme is specific to α-(1→4)-glucosidic linkage as substrates and transglucosylation products. Maltose is the most preferred substrate. Crystal structures of BspAG13_31A wild-type for the substrate-free form and inactive acid/base mutant E256Q in complexes with maltooligosaccharides were solved at 1.6-2.5 Å resolution. BspAG13_31A has a catalytic domain folded by an (β/α)8 -barrel. In subsite +1, Ala200 and His203 on β→α loop 4 and Asn258 on β→α loop 5 are involved in the recognition of maltooligosaccharides. Structural basis for specificity of GH13_31 enzymes to α-(1→4)-glucosidic linkage is first described.
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Affiliation(s)
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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40
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Bezborodkina NN, Chestnova AY, Vorobev ML, Kudryavtsev BN. Spatial Structure of Glycogen Molecules in Cells. BIOCHEMISTRY (MOSCOW) 2018; 83:467-482. [PMID: 29738682 DOI: 10.1134/s0006297918050012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Glycogen is a strongly branched polymer of α-D-glucose, with glucose residues in the linear chains linked by 1→4-bonds (~93% of the total number of bonds) and with branching after every 4-8 residues formed by 1→6-glycosidic bonds (~7% of the total number of bonds). It is thought currently that a fully formed glycogen molecule (β-particle) with the self-glycosylating protein glycogenin in the center has a spherical shape with diameter of ~42 nm and contains ~ 55,000 glucose residues. The glycogen molecule also includes numerous proteins involved in its synthesis and degradation, as well as proteins performing a carcass function. However, the type and force of bonds connecting these proteins to the polysaccharide moiety of glycogen are significantly different. This review presents the available data on the spatial structure of the glycogen molecule and its changes under various physiological and pathological conditions.
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Affiliation(s)
- N N Bezborodkina
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | - A Yu Chestnova
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| | - M L Vorobev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| | - B N Kudryavtsev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
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41
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Assaf KI, Gabel D, Zimmermann W, Nau WM. High-affinity host-guest chemistry of large-ring cyclodextrins. Org Biomol Chem 2018; 14:7702-6. [PMID: 27456317 DOI: 10.1039/c6ob01161f] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The host-guest chemistry of large-ring cyclodextrins (LRCDs) has been largely unexplored due to the lack of suitable guest molecules that bind with significant affinities to enable potential applications. Herein, we report their complexation with dodecaborate anions (B12X12(2-)), a novel class of guest molecules. The binding constants of the inorganic guests (10(4)-10(6) M(-1)) allow their classification as the first tight binders for LRCDs.
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Affiliation(s)
- Khaleel I Assaf
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
| | - Detlef Gabel
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
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42
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Physicochemical interactions of cycloamylose with phenolic compounds. Carbohydr Polym 2017; 174:980-989. [DOI: 10.1016/j.carbpol.2017.07.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 11/23/2022]
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43
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Khuntawee W, Kunaseth M, Rungnim C, Intagorn S, Wolschann P, Kungwan N, Rungrotmongkol T, Hannongbua S. Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics. J Chem Inf Model 2017; 57:778-786. [DOI: 10.1021/acs.jcim.6b00595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Manaschai Kunaseth
- National
Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chompoonut Rungnim
- National
Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Suradej Intagorn
- Department
of Mathematics, Statistics and Computer Science, Kasetsart University, Kamphaeng Saen
Campus, Nakhon Pathom 73140, Thailand
| | | | - Nawee Kungwan
- Department
of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay
Kaew Road, Muang District, Chiang Mai 50200, Thailand
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44
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Roth C, Weizenmann N, Bexten N, Saenger W, Zimmermann W, Maier T, Sträter N. Amylose recognition and ring-size determination of amylomaltase. SCIENCE ADVANCES 2017; 3:e1601386. [PMID: 28097217 PMCID: PMC5235332 DOI: 10.1126/sciadv.1601386] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 11/28/2016] [Indexed: 05/25/2023]
Abstract
Starch is a major carbon and energy source throughout all kingdoms of life. It consists of two carbohydrate polymers, branched amylopectin and linear amylose, which are sparingly soluble in water. Hence, the enzymatic breakdown by glycoside hydrolases (GHs) is of great biological and societal importance. Amylomaltases (AMs) are GHs specialized in the hydrolysis of α-1,4-linked sugar chains such as amylose. They are able to catalyze an intramolecular transglycosylation of a bound sugar chain yielding polymeric sugar rings, the cycloamyloses (CAs), consisting of 20 to 100 glucose units. Despite a wealth of data on short oligosaccharide binding to GHs, no structural evidence is available for their interaction with polymeric substrates that better represent the natural polysaccharide. We have determined the crystal structure of Thermus aquaticus AM in complex with a 34-meric CA-one of the largest carbohydrates resolved by x-ray crystallography and a mimic of the natural polymeric amylose substrate. In total, 15 glucose residues interact with the protein in an extended crevice with a length of more than 40 Å. A modified succinimide, derived from aspartate, mediates protein-sugar interactions, suggesting a biological role for this nonstandard amino acid. The structure, together with functional assays, provides unique insights into the interaction of GHs with their polymeric substrate and reveals a molecular ruler mechanism for minimal ring-size determination of CA products.
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Affiliation(s)
- Christian Roth
- Institut für Bioanalytische Chemie, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - Nicole Weizenmann
- Institut für Biochemie, Universität Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Nicola Bexten
- Institut für Chemie-Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Wolfram Saenger
- Institut für Chemie-Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Wolfgang Zimmermann
- Institut für Biochemie, Universität Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Timm Maier
- Biozentrum, Universität Basel, Biozentrum, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Norbert Sträter
- Institut für Bioanalytische Chemie, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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45
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Lonardi A, Oborský P, Hünenberger PH. Solvent-Modulated Influence of Intramolecular Hydrogen-Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alice Lonardi
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
| | - Pavel Oborský
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
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46
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Baba E, Yatsunami T, Tezuka Y, Yamamoto T. Formation and Properties of Vesicles from Cyclic Amphiphilic PS-PEO Block Copolymers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10344-10349. [PMID: 27623059 DOI: 10.1021/acs.langmuir.6b03148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Linear polystyrene-poly(ethylene oxide)-polystyrene (PS-PEO-PS) block copolymers and corresponding cyclized PS-PEO counterparts with three different PS molecular weights were synthesized and self-assembled to investigate the effects arising from the topology. Linear PS5-PEO45-PS5 (L1) and cyclic PS10-PEO45 (C1) formed micelles. As previously reported for poly(n-butyl acrylate) and PEO block copolymers, the micelles from C1 showed more than 30 °C higher phase transition temperature (cloud point, Tc) than those from L1. Linear PS10-PEO45-PS10 (L2) and cyclic PS20-PEO45 (C2) resulted in the formation of a structure called large compound micelles. Self-assembly of linear PS40-PEO48-PS40 (L3) and cyclic PS86-PEO48 (C3) lead to the formation of vesicles. The vesicles were characterized by TEM, DLS, and SLS. Remarkably, the vesicles from L3 (Tc = 69, 59, and 48 °C in the presence of 1, 5, and 10 wt % of NaCl, respectively) were found to be somewhat more thermally stable than those from C3 (Tc = 62, 52, and 43 °C in the presence of 1, 5, and 10 wt % of NaCl, respectively). This trend of the thermal stability was counterintuitively opposed to the case of the micelles. Moreover, Tc of the vesicles was controlled by the ratio of L3 and C3.
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Affiliation(s)
- Eisuke Baba
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology , O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Toshiaki Yatsunami
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology , O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yasuyuki Tezuka
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology , O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takuya Yamamoto
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology , O-okayama, Meguro-ku, Tokyo 152-8552, Japan
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University , Sapporo, Hokkaido 060-8628, Japan
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47
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Liu L, Siuda I, Richards MR, Renaud J, Kitova EN, Mayer PM, Tieleman DP, Lowary TL, Klassen JS. Structure and Stability of Carbohydrate-Lipid Interactions. Methylmannose Polysaccharide-Fatty Acid Complexes. Chembiochem 2016; 17:1571-8. [PMID: 27253157 DOI: 10.1002/cbic.201600123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 11/07/2022]
Abstract
We report a detailed study of the structure and stability of carbohydrate-lipid interactions. Complexes of a methylmannose polysaccharide (MMP) derivative and fatty acids (FAs) served as model systems. The dependence of solution affinities and gas-phase dissociation activation energies (Ea ) on FA length indicates a dominant role of carbohydrate-lipid interactions in stabilizing (MMP+FA) complexes. Solution (1) H NMR results reveal weak interactions between MMP methyl groups and FA acyl chain; MD simulations suggest the complexes are disordered. The contribution of FA methylene groups to the Ea is similar to that of heats of transfer of n-alkanes from the gas phase to polar solvents, thus suggesting that MMP binds lipids through dipole-induced dipole interactions. The MD results point to hydrophobic interactions and H-bonds with the FA carboxyl group. Comparison of collision cross sections of deprotonated (MMP+FA) ions with MD structures suggests that the gaseous complexes are disordered.
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Affiliation(s)
- Lan Liu
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Iwona Siuda
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Michele R Richards
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Justin Renaud
- Chemistry Department, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elena N Kitova
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Paul M Mayer
- Chemistry Department, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Todd L Lowary
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - John S Klassen
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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48
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Li Q, Qiu SC, Zhang J, Chen K, Huang Y, Xiao X, Zhang Y, Li F, Zhang YQ, Xue SF, Zhu QJ, Tao Z, Lindoy LF, Wei G. Twisted Cucurbit[n]urils. Org Lett 2016; 18:4020-3. [PMID: 27499014 DOI: 10.1021/acs.orglett.6b01842] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two new twisted cucurbiturils, cucurbit[13]uril (tQ[13]) and cucurbit[15]uril (tQ[15]), have been synthesized and separated, and their structures have been confirmed by NMR spectroscopy and MALDI-TOF mass spectrometry together with the X-ray structures of two new complexes, {Dy(H2O)4Cd(H2O)4tQ[13]}·2.5[CdCl4]·65H2O and {Cd0.5(H2O)2tQ[15]}·[CdCl4]·47H2O. tQ[15] is the largest cucurbit[n]uril (Q[n]) in the Q[n] family reported to date. The X-ray diffraction studies of both complexes indicated that these large tQ[n]s effectively exhibit two different cavities-a central cavity and two side cavities. Preliminary host-guest behavior by each of the new systems was investigated by NMR studies.
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Affiliation(s)
- Qing Li
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Sheng-Chao Qiu
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Jing Zhang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Kai Chen
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology , Nanjing 210044, P. R. China
| | - Ying Huang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Xin Xiao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Yingjie Zhang
- Australian Nuclear Science and Technology Organisation , Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Feng Li
- School of Science and Health, Western Sydney University , Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Yun-Qian Zhang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Sai-Feng Xue
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Qian-Jiang Zhu
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Zhu Tao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University , Guiyang, Guizhou 550025, China
| | - Leonard F Lindoy
- School of Chemistry, The University of Sydney , Sydney, NSW 2006, Australia
| | - Gang Wei
- CSIRO Manufacturing , P.O. Box 218, Lindfield, NSW 2070, Australia
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Okuyama M, Saburi W, Mori H, Kimura A. α-Glucosidases and α-1,4-glucan lyases: structures, functions, and physiological actions. Cell Mol Life Sci 2016; 73:2727-51. [PMID: 27137181 PMCID: PMC11108350 DOI: 10.1007/s00018-016-2247-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/30/2022]
Abstract
α-Glucosidases (AGases) and α-1,4-glucan lyases (GLases) catalyze the degradation of α-glucosidic linkages at the non-reducing ends of substrates to release α-glucose and anhydrofructose, respectively. The AGases belong to glycoside hydrolase (GH) families 13 and 31, and the GLases belong to GH31 and share the same structural fold with GH31 AGases. GH13 and GH31 AGases show diverse functions upon the hydrolysis of substrates, having linkage specificities and size preferences, as well as upon transglucosylation, forming specific α-glucosidic linkages. The crystal structures of both enzymes were determined using free and ligand-bound forms, which enabled us to understand the important structural elements responsible for the diverse functions. A series of mutational approaches revealed features of the structural elements. In particular, amino-acid residues in plus subsites are of significance, because they regulate transglucosylation, which is used in the production of industrially valuable oligosaccharides. The recently solved three-dimensional structure of GLase from red seaweed revealed the amino-acid residues essential for lyase activity and the strict recognition of the α-(1 → 4)-glucosidic substrate linkage. The former was introduced to the GH31 AGase, and the resultant mutant displayed GLase activity. GH13 and GH31 AGases hydrate anhydrofructose to produce glucose, suggesting that AGases are involved in the catabolic pathway used to salvage unutilized anhydrofructose.
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Affiliation(s)
- Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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50
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Khuntawee W, Rungrotmongkol T, Wolschann P, Pongsawasdi P, Kungwan N, Okumura H, Hannongbua S. Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations. Carbohydr Polym 2016; 141:99-105. [DOI: 10.1016/j.carbpol.2015.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 09/04/2015] [Accepted: 10/08/2015] [Indexed: 11/27/2022]
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