1
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Molecular dynamics study on the interaction of tricalcium silicate/polymer composites. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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Wang Z, Hu N, Zhou Y, Shi N, Shen B, Luo L, Feng J. Structure-guided affinity maturation of a novel human antibody targeting the SARS-CoV-2 nucleocapsid protein. Sci Rep 2022; 12:8469. [PMID: 35589780 PMCID: PMC9118815 DOI: 10.1038/s41598-022-12242-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/04/2022] [Indexed: 01/09/2023] Open
Abstract
The continuous mutation of SARS-CoV-2 has presented enormous challenges to global pandemic prevention and control. Recent studies have shown evidence that the genome sequence of SARS-CoV-2 nucleocapsid proteins is relatively conserved, and their biological functions are being confirmed. There is increasing evidence that the N protein will not only provide a specific diagnostic marker but also become an effective treatment target. In this study, 2G4, which specifically recognizes the N protein, was identified by screening a human phage display library. Based on the computer-guided homology modelling and molecular docking method used, the 3-D structures for the 2G4 scFv fragment (VH-linker-VL structure, with (G4S)3 as the linker peptide in the model), SARS-CoV-2 N protein and its complex were modelled and optimized with a suitable force field. The binding mode and key residues of the 2G4 and N protein interaction were predicted, and three mutant antibodies (named 2G4-M1, 2G4-M2 and 2G4-M3) with higher affinity were designed theoretically. Using directed point mutant technology, the three mutant antibodies were prepared, and their affinity was tested. Their affinity constants of approximately 0.19 nM (2G4-M1), 0.019 nM (2G4-M2) and 0.075 nM (2G4-M3) were at least one order of magnitude lower than that of the parent antibody (3 nM; 2G4, parent antibody), as determined using a biolayer interferometry (BLI) assay. It is expected that high-affinity candidates will be used for diagnosis and even as potential therapeutic drugs for the SARS-CoV-2 pandemic.
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Affiliation(s)
- Zhihong Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Naijing Hu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Yangyihua Zhou
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Ning Shi
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Beifen Shen
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Longlong Luo
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China.
| | - Jiannan Feng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China.
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3
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Wei X, Min Y, Feng Y, He D, Zeng X, Huang Y, Fan S, Chen H, Chen J, Xiang K, Luo H, Yin G, Hu D. Development and validation of an individualized nomogram for predicting the high-volume (> 5) central lymph node metastasis in papillary thyroid microcarcinoma. J Endocrinol Invest 2022; 45:507-515. [PMID: 34491546 DOI: 10.1007/s40618-021-01675-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/03/2021] [Indexed: 01/30/2023]
Abstract
PURPOSE Papillary thyroid microcarcinoma (PTMC) frequently presents a favorable clinical outcome, while aggressive invasiveness can also be found in some of this population. Identifying the risk clinical factors of high-volume (> 5) central lymph node metastasis (CLNM) in PTMC patients could help oncologists make a better-individualized clinical decision. METHODS We retrospectively reviewed the clinical characteristics of adult patients with PTC in the Surveillance, Epidemiology, and End Results (SEER) database between Jan 2010 and Dec 2015 and in one medical center affiliated to Chongqing Medical University between Jan 2018 and Oct 2020. Univariate and multivariate logistic regression analyses were used to determine the risk factors for high volume of CLNM in PTMC patients. RESULTS The male gender (OR = 2.02, 95% CI 1.46-2.81), larger tumor size (> 5 mm, OR = 1.64, 95% CI 1.13-2.38), multifocality (OR = 1.87, 95% CI 1.40-2.51), and extrathyroidal invasion (OR = 3.67; 95% CI 2.64-5.10) were independent risk factors in promoting high-volume of CLNM in PTMC patients. By contrast, elderly age (≥ 55 years) at diagnosis (OR = 0.57, 95% CI 0.40-0.81) and PTMC-follicular variate (OR = 0.60, 95% CI 0.42-0.87) were determined as the protective factors. Based on these indicators, a nomogram was further constructed with a good concordance index (C-index) of 0.702, supported by an external validating cohort with a promising C-index of 0.811. CONCLUSION A nomogram was successfully established and validated with six clinical indicators. This model could help surgeons to make a better-individualized clinical decision on the management of PTMC patients, especially in terms of whether prophylactic central lymph node dissection and postoperative radiotherapy should be warranted.
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Affiliation(s)
- X Wei
- Department of Internal Cardiology, The Second Affiliated Hospital, Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - Y Min
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - Y Feng
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - D He
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - X Zeng
- Department of Oncology, The Second Affiliated Hospital, Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - Y Huang
- Department of Pathology, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - S Fan
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - H Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - J Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - K Xiang
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - H Luo
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China
| | - G Yin
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China.
| | - D Hu
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 74, Linjiang Rd, Yuzhong Dist, Chongqing, 404100, People's Republic of China.
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4
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Lim VT, Hahn DF, Tresadern G, Bayly CI, Mobley DL. Benchmark assessment of molecular geometries and energies from small molecule force fields. F1000Res 2020; 9:Chem Inf Sci-1390. [PMID: 33604023 PMCID: PMC7863993 DOI: 10.12688/f1000research.27141.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing.
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Affiliation(s)
- Victoria T. Lim
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - David F. Hahn
- Computational Chemistry, Janssen Research & Development, Beerse, B-2340, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Beerse, B-2340, Belgium
| | | | - David L. Mobley
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
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5
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Wang T, Shang H, Zhang Q. Adsorption behavior of thiophene on MoS2 under a microwave electric field via DFT and MD studies. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Zhang Y, Fang T, Hou Q, Li Z, Yan Y. Water desalination of a new three-dimensional covalent organic framework: a molecular dynamics simulation study. Phys Chem Chem Phys 2020; 22:16978-16984. [PMID: 32676628 DOI: 10.1039/d0cp01792b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Preparing a nanoporous membrane with high density and ordered pore sizes which allows high water permeability and salt rejection rate is the key to realize highly efficient desalination. However, preparing a nanoporous membrane with high density and order pore sizes is still extremely hard due to the limitation of experimental techniques. Recently, a 3D covalent organic framework (3D-COF) material named as the 3D-OH-COF with good crystallinity and large specific surface areas has been synthesized. Based on the structural features of the 3D-OH-COF, we speculate that it may be a good candidate for the desalination application derived from its high-density sub-nanometer pore. In this work, using molecular dynamics simulations, the possibility of the 3D-OH-COF for desalination application was explored, the influence of membrane thickness on its desalination performance was also studied, and the detailed structure and dynamics of ions and water transport in the channel of the 3D-OH-COF was discussed. The results show that the rectangular channel structure and charged H atoms are responsible for the excellent salt rejection rate (100%) and high water flux (41.44 Lit cm-2 day-1 MPa-1), respectively. Furthermore, the water flux is three orders of magnitude higher than that of the commercial reverse osmosis membrane and is four times higher than that of the theoretically reported monolayer nanoporous MoS2 membrane. It is also about 28% higher than that of the recently reported 2D-CAP membrane. This work theoretically confirms that the 3D-OH-COF is a promising membrane material for desalination applications and the underlying molecular mechanisms are clarified.
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Affiliation(s)
- Yifan Zhang
- Department of Chemistry, University College London, London, UK
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7
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Abstract
There are many types of concrete protection materials, but silane-based protective materials have excellent performance and durability. Experimental usage of silane sol-based waterproof materials is relatively mature and research studies on microscale mechanisms are relatively sparse. In this paper, molecular dynamics simulations are used to explain the microscopic transmission mechanism by analyzing the transport of water molecules and siloxane molecules in the gel pores, the local structure at the interface, and the molecular dynamics in the pores. Firstly, four models with different concentrations were constructed (0, 0.3, 0.6, and 0.9 mol/L). By comparison, it can be found that as the concentration increases, so does the effect of inhibiting the transport of water molecules in the pores. Based on the determination of the concentration, this paper corrects the arrangement. Next, the three commonly used silanes in the experiment were selected for simulation. It was found that octyltriethoxysilane has good stability and a waterproof effect. Among them, octyltriethoxysilane has a longer alkyl chain and is more stable at the interface, which destroys the original spatial correlation and weakens the capillary adsorption.
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8
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Liu J, Cheng S, Cao N, Geng C, He C, Shi Q, Xu C, Ni J, DuChanois RM, Elimelech M, Zhao H. Actinia-like multifunctional nanocoagulant for single-step removal of water contaminants. NATURE NANOTECHNOLOGY 2019; 14:64-71. [PMID: 30478276 DOI: 10.1038/s41565-018-0307-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/18/2018] [Indexed: 06/09/2023]
Abstract
Current technologies for water purification are limited by their contaminant-specific removal capability, requiring multiple processes to meet water quality objectives. Here we show an innovative biomimetic micellar nanocoagulant that imitates the structure of Actinia, a marine predator that uses its tentacles to ensnare food, for the removal of an array of water contaminants with a single treatment step. The Actinia-like micellar nanocoagulant has a core-shell structure and readily disperses in water while maintaining a high stability against aggregation. To achieve effective coagulation, the nanocoagulant everts its configuration, similar to Actinia. The shell hydrolyses into 'flocs' and destabilizes and enmeshes colloidal particles while the core is exposed to water, like the extended tentacles of Actinia, and adsorbs the dissolved contaminants. The technology, with its ability to remove a broad spectrum of contaminants and produce high-quality water, has the potential to be a cost-effective replacement for current water treatment processes.
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Affiliation(s)
- Jinwei Liu
- Department of Environmental Engineering, Peking University, Beijing, China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China
| | - Shihan Cheng
- Department of Environmental Engineering, Peking University, Beijing, China
- Beijing Engineering Research Center of Advanced Wastewater Treatment, Beijing, China
| | - Na Cao
- College of Chemistry and Chemical Engineering, China University of Petroleum, Qingdao, China
| | - Chunxiang Geng
- College of Chemistry and Chemical Engineering, China University of Petroleum, Qingdao, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Chunming Xu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Jinren Ni
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, Beijing, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Ryan M DuChanois
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA.
| | - Huazhang Zhao
- Department of Environmental Engineering, Peking University, Beijing, China.
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, China.
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9
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Yu J, Li S, Hou D, Jin Z, Liu Q. Hydrophobic silane coating films for the inhibition of water ingress into the nanometer pore of calcium silicate hydrate gels. Phys Chem Chem Phys 2019; 21:19026-19038. [DOI: 10.1039/c9cp03266e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Water molecule capillary transport is inhibited via the nanometer channel of calcium silicate hydrate (C–S–H) with the interior surface impregnated with silane.
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Affiliation(s)
- Jiao Yu
- Department of Civil Engineering
- Qingdao University of Technology
- Qingdao 266000
- China
| | - Shaochun Li
- Department of Civil Engineering
- Qingdao University of Technology
- Qingdao 266000
- China
| | - Dongshuai Hou
- Department of Civil Engineering
- Qingdao University of Technology
- Qingdao 266000
- China
| | - Zuquan Jin
- Department of Civil Engineering
- Qingdao University of Technology
- Qingdao 266000
- China
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10
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He X, Lu J, Desanker M, Invergo AM, Lohr TL, Ren N, Lockwood FE, Marks TJ, Chung YW, Wang QJ. Boundary Lubrication Mechanisms for High-Performance Friction Modifiers. ACS APPLIED MATERIALS & INTERFACES 2018; 10:40203-40211. [PMID: 30396273 DOI: 10.1021/acsami.8b11075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We recently reported a new molecular heterocyclic friction modifier (FM) that exhibits excellent friction and wear reduction in the boundary lubrication regime. This paper explores the mechanisms by which friction reduction occurs with heterocyclic alkyl-cyclen FM molecules. We find that these chelating molecules adsorb onto (oxidized) steel surfaces far more tenaciously than conventional FMs such as simple alkylamines. Molecular dynamics simulations argue that the surface coverage of our heterocyclic FM molecules remains close to 100% even at 200 °C. This thermal stability allows the FMs to firmly anchor to the surface, allowing the hydrocarbon chains of the molecules to interact and trap base oil lubricant molecules. This results in thicker boundary film thickness compared with conventional FMs, as shown by optical interferometry measurements.
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Affiliation(s)
| | | | | | | | | | - Ning Ren
- Valvoline Inc., Lexington , Kentucky 40512 , United States
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11
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Martins F, Freitas MP. Revisiting the Case of an Intramolecular Hydrogen Bond Network Forming Four- and Five-Membered Rings in d-Glucose. ACS OMEGA 2018; 3:10250-10254. [PMID: 31459154 PMCID: PMC6645413 DOI: 10.1021/acsomega.8b01455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/20/2018] [Indexed: 05/11/2023]
Abstract
The conformational behavior of cyclic monosaccharides has been widely studied over the past years, but there is no general agreement about which effects are in fact responsible for the observed conformational preferences. A recent microwave spectroscopy study determined the conformational equilibrium of d-glucose in the gas phase with a preference for a counterclockwise arrangement of the hydroxyl groups. Nevertheless, the effects that control this orientation are still uncertain because the role of intramolecular hydrogen bonds (IHBs), electrostatic and steric repulsions is not clear. This work reports a density functional theory approach based on the conformational energies of d-glucose and of some derivatives in which the anomeric hydroxyl is replaced with hydrogen (H, small and not prone to participate in proton transfer), fluorine (F, small, electronegative, and as capable as OH of forming hydrogen bonds as a proton acceptor), and chlorine (Cl, big and not anticipated to be involved in effective hydrogen bond formation) to obtain insights into the effects of the substituent at the anomeric carbon on the arrangement of the hydroxyl groups in d-glucose. The nature of the substituents at this position is crucial to determine the orientation of the remaining hydroxyl groups. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses, in addition to NMR chemical shift calculations, have been provided to support the conformational energy outcomes. Overall, the results agree with the lack of IHBs forming four- and five-membered rings in d-glucose and emphasize that steric and electrostatic repulsions involving the hydroxyl groups in the clockwise orientation are driving forces of the conformational behavior.
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12
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Zhou Y, Hou D, Manzano H, Orozco CA, Geng G, Monteiro PJM, Liu J. Interfacial Connection Mechanisms in Calcium-Silicate-Hydrates/Polymer Nanocomposites: A Molecular Dynamics Study. ACS APPLIED MATERIALS & INTERFACES 2017; 9:41014-41025. [PMID: 29076343 DOI: 10.1021/acsami.7b12795] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Properties of organic/inorganic composites can be highly dependent on the interfacial connections. In this work, molecular dynamics, using pair-potential-based force fields, was employed to investigate the structure, dynamics, and stability of interfacial connections between calcium-silicate-hydrates (C-S-H) and organic functional groups of three different polymer species. The calculation results suggest that the affinity between C-S-H and polymers is influenced by the polarity of the functional groups and the diffusivity and aggregation tendency of the polymers. In the interfaces, the calcium counterions from C-S-H act as the coordination atoms in bridging the double-bonded oxygen atoms in the carboxyl groups (-COOH), and the Ca-O connection plays a dominant role in binding poly(acrylic acid) (PAA) due to the high bond strength defined by time-correlated function. The defective calcium-silicate chains provide significant numbers of nonbridging oxygen sites to accept H-bonds from -COOH groups. As compared with PAA, the interfacial interactions are much weaker between C-S-H and poly(vinyl alcohol) (PVA) or poly(ethylene glycol) (PEG). Predominate percentage of the -OH groups in the PVA form H-bonds with inter- and intramolecule, which results in the polymer intertwining and reduces the probability of H-bond connections between PVA and C-S-H. On the other hand, the inert functional groups (C-O-C) in poly(ethylene glycol) (PEG) make this polymer exhibit unfolded configurations and move freely with little restrictions. The interaction mechanisms interpreted in this organic-inorganic interface can give fundamental insights into the polymer modification of C-S-H and further implications to improving cement-based materials from the genetic level.
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Affiliation(s)
- Yang Zhou
- School of Materials Science and Engineering, Southeast University , Nanjing 211189, China
- Department of Civil and Environmental Engineering, University of California , Berkeley, California 94720, United States
- State Key Laboratory of High Performance Civil Engineering Materials, Jiangsu Research Institute of Building Science Co. , Nanjing 211103, China
| | - Dongshuai Hou
- School of Civil Engineering, Qingdao Technological University , Qingdao 266033, China
| | - Hegoi Manzano
- Department of Condensed Matter Physics, University of the Basque Country UPV/EHU , Barrio Sarriena s/n, 48960 Leioa, Spain
| | - Carlos A Orozco
- Department of Civil and Environmental Engineering, University of California , Berkeley, California 94720, United States
| | - Guoqing Geng
- Department of Civil and Environmental Engineering, University of California , Berkeley, California 94720, United States
| | - Paulo J M Monteiro
- Department of Civil and Environmental Engineering, University of California , Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Jiaping Liu
- School of Materials Science and Engineering, Southeast University , Nanjing 211189, China
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13
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Shamloo A, Sarmadi M. Investigation of the adhesive characteristics of polymer–protein systems through molecular dynamics simulation and their relation to cell adhesion and proliferation. Integr Biol (Camb) 2016; 8:1276-1295. [DOI: 10.1039/c6ib00159a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
| | - Morteza Sarmadi
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
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14
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Canales Á, Mallagaray Á, Berbís MÁ, Navarro-Vázquez A, Domínguez G, Cañada FJ, André S, Gabius HJ, Pérez-Castells J, Jiménez-Barbero J. Lanthanide-Chelating Carbohydrate Conjugates Are Useful Tools To Characterize Carbohydrate Conformation in Solution and Sensitive Sensors to Detect Carbohydrate–Protein Interactions. J Am Chem Soc 2014; 136:8011-7. [DOI: 10.1021/ja502406x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ángeles Canales
- Department
of Química Orgánica I, Fac. C.C. Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n 28040, Madrid, Spain
| | - Álvaro Mallagaray
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - M. Álvaro Berbís
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Armando Navarro-Vázquez
- Department
of Química Orgánica, Universidade de Vigo, Campus Universitario
Vigo, 36310, Pontevedra, Spain
| | - Gema Domínguez
- Faculty
of De Farmacia, Department of Química, Universidad CEU San Pablo, Urb. Montepríncipe, ctra. Boadilla del Monte, 28668, Madrid, Spain
| | - F. Javier Cañada
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Sabine André
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539, Munich, Germany
| | - Hans-Joachim Gabius
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539, Munich, Germany
| | - Javier Pérez-Castells
- Faculty
of De Farmacia, Department of Química, Universidad CEU San Pablo, Urb. Montepríncipe, ctra. Boadilla del Monte, 28668, Madrid, Spain
| | - Jesús Jiménez-Barbero
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
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15
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Sakhavand N, Muthuramalingam P, Shahsavari R. Toughness governs the rupture of the interfacial H-bond assemblies at a critical length scale in hybrid materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8154-8163. [PMID: 23713817 DOI: 10.1021/la4014015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The geometry and material property mismatch across the interface of hybrid materials with dissimilar building blocks make it extremely difficult to fully understand the lateral chemical bonding processes and design nanocomposites with optimal performance. Here, we report a combined first-principles study, molecular dynamics modeling, and theoretical derivations to unravel the detailed mechanisms of H-bonding, deformation, load transfer, and failure at the interface of polyvinyl alcohol (PVA) and silicates, as an example of hybrid materials with geometry and property mismatch across the interface. We identify contributing H-bonds that are key to adhesion and demonstrate a specific periodic pattern of interfacial H-bond network dictated by the interface mismatch and intramolecular H-bonding. We find that the maximum toughness, incorporating both intra- and interlayer strain energy contributions, govern the existence of optimum overlap length and thus the rupture of interfacial (interlayer) H-bond assemblies in natural and synthetic hybrid materials. This universally valid result is in contrast to the previous reports that correlate shear strength with rupture of H-bonds assemblies at a finite overlap length. Overall, this work establishes a unified understanding to explain the interplay between geometric constraints, interfacial H-bonding, materials characteristics, and optimal mechanical properties in hybrid organic-inorganic materials.
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Affiliation(s)
- Navid Sakhavand
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, USA
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16
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Regis S, Youssefian S, Jassal M, Phaneuf MD, Rahbar N, Bhowmick S. Fibronectin adsorption on functionalized electrospun polycaprolactone scaffolds: Experimental and molecular dynamics studies. J Biomed Mater Res A 2013; 102:1697-706. [DOI: 10.1002/jbm.a.34843] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 06/04/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Shawn Regis
- Biomedical Engineering and Biotechnology Program; University of Massachusetts Dartmouth; North Dartmouth Massachusetts 02747
| | - Sina Youssefian
- Department of Mechanical Engineering; Worcester Polytechnic Institute; Worcester Massachusetts 01609
| | - Manisha Jassal
- Biomedical Engineering and Biotechnology Program; University of Massachusetts Dartmouth; North Dartmouth Massachusetts 02747
| | | | - Nima Rahbar
- Department of Civil and Environmental Engineering; Worcester Polytechnic Institute; Worcester Massachusetts 01609
| | - Sankha Bhowmick
- Biomedical Engineering and Biotechnology Program; University of Massachusetts Dartmouth; North Dartmouth Massachusetts 02747
- Department of Mechanical Engineering; University of Massachusetts Dartmouth; North Dartmouth Massachusetts 02747
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Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
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Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
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Raffaini G, Ganazzoli F. A molecular modeling study of complex formation and self-aggregation behavior of a porphyrin–β-cyclodextrin conjugate. J INCL PHENOM MACRO 2012. [DOI: 10.1007/s10847-012-0193-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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20
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Nomme J, Renodon-Cornière A, Asanomi Y, Sakaguchi K, Stasiak AZ, Stasiak A, Norden B, Tran V, Takahashi M. Design of potent inhibitors of human RAD51 recombinase based on BRC motifs of BRCA2 protein: modeling and experimental validation of a chimera peptide. J Med Chem 2010; 53:5782-91. [PMID: 20684611 PMCID: PMC2917172 DOI: 10.1021/jm1002974] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have previously shown that a 28-amino acid peptide derived from the BRC4 motif of BRCA2 tumor suppressor inhibits selectively human RAD51 recombinase (HsRad51). With the aim of designing better inhibitors for cancer treatment, we combined an in silico docking approach with in vitro biochemical testing to construct a highly efficient chimera peptide from eight existing human BRC motifs. We built a molecular model of all BRC motifs complexed with HsRad51 based on the crystal structure of the BRC4 motif-HsRad51 complex, computed the interaction energy of each residue in each BRC motif, and selected the best amino acid residue at each binding position. This analysis enabled us to propose four amino acid substitutions in the BRC4 motif. Three of these increased the inhibitory effect in vitro, and this effect was found to be additive. We thus obtained a peptide that is about 10 times more efficient in inhibiting HsRad51-ssDNA complex formation than the original peptide.
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Affiliation(s)
- Julian Nomme
- UMR 6204 U-3B, Centre National de la Recherche Scientifique & Universite de Nantes, France
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21
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Raffaini G, Ganazzoli F. A molecular dynamics study of the inclusion complexes of C60 with some cyclodextrins. J Phys Chem B 2010; 114:7133-9. [PMID: 20450215 DOI: 10.1021/jp911812j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The strongly hydrophobic C(60) fullerene is a carbon allotrope of huge interest in materials science and in pharmaceutical chemistry that can be solubilized in water either by extensive chemical functionalization or by inclusion in appropriate carriers such as the cyclodextrins with formation of host-guest complexes. Here we report a molecular dynamics study of the complexes formed in solution by C(60) with gamma- and delta-cyclodextrins. The most stable host-guest complex stoichiometry is determined to be 2:1 through simulations in vacuo and in explicit water by the stepwise addition of the cyclodextrins to C(60). No a priori assumption about the inclusion stoichiometry and geometry is made. The equilibrium fluctuations of the complexes that can affect the system stability are also investigated within the molecular dynamics runs.
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Affiliation(s)
- Giuseppina Raffaini
- Dipartimento di Chimica, Materiali e Ingegneria Chimica G. Natta, Politecnico di Milano, via L. Mancinelli 7, 20131 Milano, Italy.
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22
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Schnupf U, Willett J, Momany F. DFTMD studies of glucose and epimers: anomeric ratios, rotamer populations, and hydration energies. Carbohydr Res 2010; 345:503-11. [DOI: 10.1016/j.carres.2009.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/24/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
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23
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. COMPREHENSIVE NATURAL PRODUCTS II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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24
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Muñoz FJ, Santos JI, Ardá A, André S, Gabius HJ, Sinisterra JV, Jiménez-Barbero J, Hernáiz MJ. Binding studies of adhesion/growth-regulatory galectins with glycoconjugates monitored by surface plasmon resonance and NMR spectroscopy. Org Biomol Chem 2010; 8:2986-92. [DOI: 10.1039/b927139b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Jiménez-Barbero J, Dragoni E, Venturi C, Nannucci F, Ardá A, Fontanella M, André S, Cañada FJ, Gabius HJ, Nativi C. Alpha-O-linked glycopeptide mimetics: synthesis, conformation analysis, and interactions with viscumin, a galactoside-binding model lectin. Chemistry 2009; 15:10423-31. [PMID: 19746469 DOI: 10.1002/chem.200901077] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Efficient cycloaddition of a silylidene-protected galactal with a suitable heterodiene yielded the basis for a facile diastereoselective route to a glycopeptide-mimetic scaffold. Its carbohydrate part was further extended by beta1-3-linked galactosylation. The pyranose rings retain their (4)C(1) chair conformation, as shown by molecular modeling and NMR spectroscopy, and the typical exo-anomeric geometry was observed for the disaccharide. The expected bioactivity was ascertained by saturation-transfer-difference NMR spectroscopy by using the galactoside-specific plant toxin viscumin as a model lectin. The experimental part was complemented by molecular docking. The described synthetic route and the strategic combination of computational and experimental techniques to reveal conformational properties and bioactivity establish the prepared alpha-O-linked glycopeptide mimetics as promising candidates for further exploitation of this scaffold to give O-glycans for lectin blocking and vaccination.
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Affiliation(s)
- Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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26
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Raffaini G, Ganazzoli F, Malpezzi L, Fuganti C, Fronza G, Panzeri W, Mele A. Validating a strategy for molecular dynamics simulations of cyclodextrin inclusion complexes through single-crystal X-ray and NMR experimental data: a case study. J Phys Chem B 2009; 113:9110-22. [PMID: 19526998 DOI: 10.1021/jp901581e] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A theoretical and experimental study about the formation and structure of the inclusion complex (-)-menthyl-O-beta-D-glucopyranoside 1 with beta-cyclodextrin (beta-CD) 2 is presented as paradigmatic case study to test the results of molecular dynamics (MD) simulations. The customary methodological approach-the use of experimental geometrical parameters as restraints for MD runs-is logically reversed and the calculated structures are a posteriori compared with those obtained from NMR spectroscopy in D(2)O solution and single crystal X-ray diffraction so as to validate the simulation procedure. The guest molecule 1 allows for a broad repertoire of intermolecular interactions (dipolar, hydrophobic, hydrogen bonds) concurring to stabilize the host-guest complex, thus providing the general applicability of the simulation procedure to cyclodextrin physical chemistry. Many starting geometries of the host-guest association were chosen, not assuming any a priori inclusion. The simulation protocol, involving energy minimization and MD runs in explicit water, yielded four possible inclusion geometries, ruling out higher-energy outer adducts. By analysis of the average energy at room temperature, the most stable geometry in solution was eventually obtained, while the kinetics of formation showed that it is also kinetically favored. The reliability of such geometry was thoroughly checked against the NOE distances via the pair distribution functions, that is, the statistical distribution of intermolecular distances among selected diagnostic atoms calculated from the MD trajectories at room temperature. An analogous procedure was adopted both with implicit solvent and in vacuo. The most stable geometry matched that found with explicit solvent but major differences were observed in the relative stability of the metastable complexes as a consequence of the lack of hydration on the polar moiety of the guest. Finally, a control set of geometrical parameters of the thermodynamically favored complex matched the corresponding one obtained from the X-ray structure, while local conformational differences were indicative of packing effects.
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Affiliation(s)
- Giuseppina Raffaini
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via L. Mancinelli 7, 20131 Milano, Italy.
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27
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Arsequell G, Salvatella M, Valencia G, Fernández-Mayoralas A, Fontanella M, Venturi C, Jiménez-Barbero J, Marrón E, Rodríguez RE. Synthesis, conformation, and biological characterization of a sugar derivative of morphine that is a potent, long-lasting, and nontolerant antinociceptive. J Med Chem 2009; 52:2656-66. [PMID: 19351163 DOI: 10.1021/jm8011245] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A synthetic mannoside derivative, namely, 6-morphinyl-alpha-D-mannopyranoside, shows a naloxone-reversible antinociception that is 100-fold more potent and twice as long lasting compared to morphine when administered intraperitoneally to rats in paw pressure and tail flick tests. The compound does not produce tolerance and binds to rat mu opioid receptors with twice the affinity of morphine. NMR studies suggest that differences of activity between the derivative and its parent compound M6G might be related to their differing molecular dynamic behavior.
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Affiliation(s)
- Gemma Arsequell
- Unit of Glycoconjugate Chemistry, Instituto de Química Avanzada de Cataluña (IQAC-CSIC), Barcelona, Jordi Girona 18-26, E08034-Barcelona, Spain
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28
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Kolympadi M, Fontanella M, Venturi C, André S, Gabius HJ, Jiménez-Barbero J, Vogel P. Synthesis and Conformational Analysis of (α-D-Galactosyl)phenylmethane and α-,β-Difluoromethane Analogues: Interactions with the Plant Lectin Viscumin. Chemistry 2009; 15:2861-73. [DOI: 10.1002/chem.200801394] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Muñoz FJ, Pérez J, Rumbero Á, Santos JI, Cañada FJ, André S, Gabius HJ, Jiménez-Barbero J, Sinisterra JV, Hernáiz MJ. Glycan Tagging to Produce Bioactive Ligands for a Surface Plasmon Resonance (SPR) Study via Immobilization on Different Surfaces. Bioconjug Chem 2009; 20:673-82. [DOI: 10.1021/bc800350q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Javier Muñoz
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - José Pérez
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - Ángel Rumbero
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - J. Ignacio Santos
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - F. Javier Cañada
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - Sabine André
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - Hans-Joachim Gabius
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - Jesús Jiménez-Barbero
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - José V. Sinisterra
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - María J. Hernáiz
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
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Fernández de Córdoba FJ, Rodríguez-Carvajal MA, Tejero-Mateo P, Gil-Serrano AM. Structure and Conformational Studies of the Disaccharides Derived from the Inner Core of the Lipopolysaccharide Isolated fromSinorhizobium frediiSMH12. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Fernández de Córdoba FJ, Rodríguez-Carvajal MA, Cañada FJ, Tejero-Mateo P, Gil-Serrano AM, Jiménez-Barbero J. Solution Conformation and Dynamics of the O-Antigen of the Major Lipopolysaccharide fromSinorhizobium frediiSMH12. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Versatile strategy for the synthesis of biotin-labelled glycans, their immobilization to establish a bioactive surface and interaction studies with a lectin on a biochip. Glycoconj J 2008; 25:633-46. [DOI: 10.1007/s10719-008-9115-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2007] [Revised: 01/25/2008] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
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33
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Denton RW, Tony KA, Hernández-Gay JJ, Cañada FJ, Jiménez-Barbero J, Mootoo DR. Synthesis and conformational behavior of the difluoromethylene linked C-glycoside analog of beta-galactopyranosyl-(1<-->1)-alpha-mannopyranoside. Carbohydr Res 2007; 342:1624-35. [PMID: 17601514 PMCID: PMC2084073 DOI: 10.1016/j.carres.2007.06.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 10/23/2022]
Abstract
C-Glycosides in which the pseudoglycosidic substituent is a methylene group have been advertised as hydrolytically stable mimetics of their parent O-glycosides. While this substitution assures greater stability, the lower polarity and increased conformational flexibility in the intersaccharide linker brought about by this change may compromise biological mimicry. In this regard, C-glycosides, in which the pseudoanomeric methylene is replaced with a difluoromethylene group, are interesting because the CF2 group is more of an isopolar replacement for oxygen than CH2. In addition, the CF2 residue is expected to instill conformational bias into the intersaccharide torsions. Herein is described the synthesis and conformational behavior of the difluoromethylene linked C-glycoside of beta-D-galactopyranosyl-(1<-->1)-alpha-D-mannopyranoside. The synthesis centers on the formation of the galactose residue via an oxocarbenium ion-enol ether cyclization. Conformational analysis, using a combination of molecular mechanics, dynamics, and NMR spectroscopy, suggests that the difluoro-C-glycoside populates the non-exo-Gal/exo-Man conformer to a major extent (ca 50%), with a minor contribution ( approximately 15%) from the exo-Gal/exo-Man conformer that corresponds to the ground sate of the parent O-glycoside.
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Affiliation(s)
- Richard W Denton
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10021, USA
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Raffaini G, Ganazzoli F. Understanding the Performance of Biomaterials through Molecular Modeling: Crossing the Bridge between their Intrinsic Properties and the Surface Adsorption of Proteins. Macromol Biosci 2007; 7:552-66. [PMID: 17477442 DOI: 10.1002/mabi.200600278] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Molecular modeling and computer simulations can yield significant new insight at the atomistic level about the performance of biomaterials in a biological environment. In this paper, we review our approach to a consistent theoretical picture of the bulk and surface properties of biomaterials. The predicted properties do encompass in particular the mechanical behavior and the surface hydration of these materials, and the surface physisorption of proteins, or polypeptides in general. The behavior of nanomaterials such as the carbon allotropes, nanotubes and fullerenes, in a biological environment is also briefly considered.
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Affiliation(s)
- Giuseppina Raffaini
- Dipartimento di Chimica, Materiali e Ingegneria Chimica G. Natta, Politecnico, via L. Mancinelli 7, 20131 Milano, Italy
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35
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Pérez-Castells J, Hernández-Gay JJ, Denton RW, Tony KA, Mootoo DR, Jiménez-Barbero J. The conformational behaviour and P-selectin inhibition of fluorine-containing sialyl LeX glycomimetics. Org Biomol Chem 2007; 5:1087-92. [PMID: 17377662 DOI: 10.1039/b615752a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of experimental J/NOE NMR data with molecular mechanics and dynamics calculations has been used to examine the conformational behaviour and assign the configuration of synthetically prepared epimeric 3-carboxymethyl-O-Gal-(1-->1)-alpha-Man-fluoro-C-glycosides. It is shown that the population distributions around the glycosidic linkages strongly depend on the configuration at the fluorinated carbon of the pseudoacetal residue. It is also shown that these compounds resemble the inhibition ability of sialyl LeX towards P-selectin.
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Affiliation(s)
- Javier Pérez-Castells
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain. .
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36
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Raffaini G, Ganazzoli F. Hydration and flexibility of α-, β-, γ- and δ-cyclodextrin: A molecular dynamics study. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.01.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Corzana F, Cuesta I, Freire F, Revuelta J, Torrado M, Bastida A, Jiménez-Barbero J, Asensio JL. The Pattern of Distribution of Amino Groups Modulates the Structure and Dynamics of Natural Aminoglycosides: Implications for RNA Recognition. J Am Chem Soc 2007; 129:2849-65. [PMID: 17298063 DOI: 10.1021/ja066348x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aminoglycosides are clinically relevant antibiotics that participate in a large variety of molecular recognition processes involving different RNA and protein receptors. The 3-D structures of these policationic oligosaccharides play a key role in RNA binding and therefore determine their biological activity. Herein, we show that the particular NH2/NH3(+)/OH distribution within the antibiotic scaffold modulates the oligosaccharide conformation and flexibility. In particular, those polar groups flanking the glycosidic linkages have a significant influence on the antibiotic structure. A careful NMR/theoretical analysis of different natural aminoglycosides, their fragments, and synthetic derivatives proves that both hydrogen bonding and charge-charge repulsive interactions are at the origin of this effect. Current strategies to obtain new aminoglycoside derivatives are mainly focused on the optimization of the direct ligand/receptor contacts. Our results strongly suggest that the particular location of the NH2/NH3(+)/OH groups within the antibiotics can also modulate their RNA binding properties by affecting the conformational preferences and inherent flexibility of these drugs. This fact should also be carefully considered in the design of new antibiotics with improved activity.
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Affiliation(s)
- Francisco Corzana
- Contribution from the Instituto de Química OrgAnica General and Centro de Investigaciones Biológicas (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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38
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Redaelli A, Vesentini S, Soncini M, Vena P, Mantero S, Montevecchi FM. Possible role of decorin glycosaminoglycans in fibril to fibril force transfer in relative mature tendons—a computational study from molecular to microstructural level. J Biomech 2003; 36:1555-69. [PMID: 14499303 DOI: 10.1016/s0021-9290(03)00133-7] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Experimental studies on immature tendons have shown that the collagen fibril net is discontinuous. Manifold evidences, despite not being conclusive, indicate that mature tissue is discontinuous as well. According to composite theory, there is no requirement that the fibrils should extend from one end of the tissue to the other; indeed, an interfibrillar matrix with a low elastic modulus would be sufficient to guarantee the mechanical properties of the tendon. Possible mechanisms for the stress-transfer involve the interfibrillar proteoglycans and can be related to the matrix shear stress and to electrostatic non-covalent forces. Recent studies have shown that the glycosaminoglycans (GAGs) bound to decorin act like bridges between contiguous fibrils connecting adjacent fibril every 64-68 nm; this architecture would suggest their possible role in providing the mechanical integrity of the tendon structure. The present paper investigates the ability of decorin GAGs to transfer forces between adjacent fibrils. In order to test this hypothesis the stiffness of chondroitin-6-sulphate, a typical GAG associated to decorin, has been evaluated through the molecular mechanics approach. The obtained GAG stiffness is piecewise linear with an initial plateau at low strains (<800%) and a high stiffness region (3.1 x 10(-11)N/nm) afterwards. By introducing the calculated GAG stiffness in a multi-fibril model, miming the relative mature tendon architecture, the stress-strain behaviour of the collagen fibre was determined. The fibre incremental elastic modulus obtained ranges between 100 and 475 MPa for strains between 2% and 6%. The elastic modulus value depends directly on the fibril length, diameter and inversely on the interfibrillar distance. In particular, according to the obtained results, the length of the fibril is likely to play the major role in determining stiffness in mature tendons.
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Affiliation(s)
- A Redaelli
- Department of Bioengineering, Politecnico di Milano, Via Golgi 39, 20133 Milan, Italy.
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39
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Sillerud LO, Burks EJ, Wester MJ, Brown DC, Vijayan S, Larson RS. NMR-derived model of interconverting conformations of an ICAM-1 inhibitory cyclic nonapeptide. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2003; 62:97-116. [PMID: 12895272 DOI: 10.1034/j.1399-3011.2003.00070.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have produced by phage-display a disulfide-linked cyclic nonapeptide (inhibitory peptide-01, IP01), CLLRMRSIC, that binds to intracellular adhesion molecule-1 (ICAM-1) and blocks binding to its counter-structure, leukocyte functional antigen-1 (LFA-1). As a first step towards improving its pharmacologic properties, we have performed a structural and functional analysis of this peptide inhibitor to determine the features relevant to ICAM-1 binding. We report here the solution model of our initial product, IP01, as derived from two-dimensional nuclear magnetic resonance (NMR) restraints and molecular modeling. Distance and dihedral angle restraints, generated from nuclear Overhauser effect spectroscopy (NOESY) and one-dimensional-NMR experiments respectively, were used to generate an ensemble of structures using distance geometry and simulated annealing. Molecular dynamic simulations produced three interconverting conformational families consistent with the NMR-derived constraints. We describe these conformations and their mechanism of interconversion. Furthermore, we have measured the IC50 s of a series of inhibitors generated from IP01 through alanine substitution of each residue. These results show that the L2-L3-R4-M5-R6 segment is functionally active, conformationally flexible, and contains a beta-turn involving residues R4-S7, while the C1-C9-I8-S7 segment is less functionally-active but adopts a more defined solution conformation, consistent with a scaffolding function. This model will be useful for designing nonpeptide-based organic inhibitors with improved pharmacologic properties.
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Affiliation(s)
- L O Sillerud
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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40
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Strati GL, Willett JL, Momany FA. Ab initio computational study of beta-cellobiose conformers using B3LYP/6-311++G**. Carbohydr Res 2002; 337:1833-49. [PMID: 12431885 DOI: 10.1016/s0008-6215(02)00267-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The molecular structure of 27 conformers of beta-cellobiose were studied in vacuo through gradient geometry optimization using B3LYP density functionals and the 6-311++G** basis set. The conformationally dependent geometry changes and energies were explored as well as the hydrogen-bonding network. The lowest electronic energy structures found were not those suggested from available crystallographic and NMR solution data, where the glycosidic dihedral angles fall in the region (phi, psi) approximately (40 degrees, -20 degrees ). Rather, 'flipped' conformations in which the dihedral angles are in the range (phi, psi) approximately (180 degrees, 0 degrees ) are energetically more stable by approximately 2.5 kcal/mol over the 'experimentally accepted' structure. Further, when the vibrational free energy, deltaG, obtained from the calculated frequencies, is compared throughout the series, structures with (phi, psi) in the experimentally observed range still have higher free energy ( approximately 2.0 kcal/mol) than 'flipped' forms. The range of bridging dihedral angles of the 'normal' conformers, resulting from the variance in the phi dihedral is larger than that found in the 'flipped' forms. Due to this large flat energy surface for the normal conformations, we surmise that the summation of populations of these conformations will favor the 'normal' conformations, although evidence suggests that polar solvent effects may play the dominant role in providing stability for the 'normal' forms. Even though some empirical studies previously found the 'flipped' conformations to be lowest in energy, these studies have been generally discredited because they were in disagreement with experimental results. Most of the DFT/ab initio conformations reported here have not been reported previously in the ab initio literature, in part because the use of less rigorous theoretical methods, i.e. smaller basis sets, have given results in general agreement with experimental data, that is, they energetically favored the 'normal' forms. These are the first DFT/ab initio calculations at this level of theory, apparently because of the length and difficulty of carrying out optimizations at these high levels.
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Affiliation(s)
- Gina L Strati
- Plant Polymer Research, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University St., Peoria, IL 61604, USA
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41
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Kim H, Jeong K, Lee S, Jung S. Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A). J Comput Aided Mol Des 2002; 16:601-10. [PMID: 12602953 DOI: 10.1023/a:1021923815450] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (1 --> 2)-beta-D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of phi-psi energy map, and the values of radius of gyration (R(G)) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.
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Affiliation(s)
- Hyunmyung Kim
- Department of Microbial Engineering, and Bio/Molecular Informatics Center, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, South Korea
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42
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Abstract
The glycosaminoglycans heparin and heparan sulfate contain similar structural units in varying proportions providing considerable diversity in sequence and biological function. Both compounds are alternating copolymers of glucosamine with both iduronate- and glucuronate-containing sequences bearing N-sulfate, N-acetyl, and O-sulfate substitution. Protein recognition of these structurally-diverse compounds depends upon substitution pattern, overall molecular shape, and on internal mobility. In this review particular attention is paid to the dynamic aspects of heparin/heparan sulfate conformation. The iduronate residue possesses an unusually flexible pyranose ring conformation. This extra source of internal mobility creates special problems in rationalization of experimental data for these compounds. We present herein the solution-state NMR parameters, fiber diffraction data, crystallographic data, and molecular modeling methods employed in the investigation of heparin and heparan sulfate. Heparin is a useful model compound for the sulfated, protein-binding regions of heparan sulfate. The literature contains a number of solution and solid-state studies of heparin oligo- and polysaccharides for both isolated heparin species and those bound to protein receptors. These studies indicate a diversity of iduronate ring conformations, but a limited range of glycosidic linkage geometries in the repeating disaccharides. In this sense, heparin exhibits a well-defined overall shape within which iduronate ring forms can freely interconvert. Recent work suggests that computational modeling could potentially identify heparin binding sites on protein surfaces.
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Affiliation(s)
- B Mulloy
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
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43
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Frecer V, Ho B, Ding JL. Molecular dynamics study on lipid A from Escherichia coli: insights into its mechanism of biological action. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1466:87-104. [PMID: 10825434 DOI: 10.1016/s0005-2736(00)00174-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Structural properties of the Escherichia coli lipid A moiety were analysed by means of molecular mechanics and molecular dynamics simulations and compared to synthetic monophospho and dephospho analogues with different biological activities in the Limulus assay. The conformation of glucosamine disaccharide headgroup, order and packing of fatty acid chains, solvation of phosphate groups, coordination by water molecules, sodium counterions and models of cationic amino acid side chains were described in terms of mean values, mean residence times, radial distribution functions, coordination numbers, solvation and interaction energies. Solvation and polar interactions of the phosphate groups were correlated to known biological activities the lipid A variants. The observed relationship between the biological effect and the number and position of the phosphate groups were explained with the help of simple mechanistic models of lipid A action. The possible mechanism of action involving specific binding of lipid A disaccharide headgroup to cationic residues of a receptor model was compared with an alternative mechanism, which assumes a relationship between the ability to adopt non-lamellar supramolecular structures and the biological activity. Conclusions are drawn about the probable mode of lipid A action. Implications for rational drug design of endotoxin-neutralising agents are discussed.
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Affiliation(s)
- V Frecer
- Departmnt of Biological Sciences, Faculty of Science, Naitonal University of Singapore, Singapore
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44
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Frecer V, Ho B, Ding JL. Interpretation of biological activity data of bacterial endotoxins by simple molecular models of mechanism of action. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:837-52. [PMID: 10651822 DOI: 10.1046/j.1432-1327.2000.01069.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lipid A moiety has been identified as the bioactive component of bacterial endotoxins (lipopolysaccharides). However, the molecular mechanism of biological activity of lipid A is still not fully understood. This paper contributes to understanding of the molecular mechanism of action of bacterial endotoxins by comparing molecular modelling results for two possible mechanisms with the underlying experimental data. Mechanisms of action involving specific binding of lipid A to a protein receptor as well as nonspecific intercalation into phospholipid membrane of a host cell were modelled and analysed. As the cellular receptor for endotoxin has not been identified, a model of a peptidic pseudoreceptor was proposed, based on molecular structure, symmetry of the lipid A moiety and the observed character of endotoxin-binding sites in proteins. We have studied the monomeric form of lipid A from Escherichia coli and its seven synthetic analogues with varying numbers of phosphate groups and correlated them with known biological activities determined by the Limulus assay. Gibbs free energies associated with the interaction of lipid A with the pseudoreceptor model and intercalation into phospholipid membrane calculated by molecular mechanics and molecular dynamics methods were used to compare the two possible mechanisms of action. The results suggest that specific binding of lipid A analogues to the peptidic pseudoreceptor carrying an amphipathic cationic binding pattern BHPHB (B, basic; H, hydrophobic; P, polar residue, respectively) is energetically more favourable than intercalation into the phospholipid membrane. In addition, binding affinities of lipid A analogues to the best minimum binding sequence KFSFK of the pseudoreceptor correlated with the experimental Limulus activity parameter. This correlation enabled us to rationalize the observed relationship between the number and position of the phosphate groups in the lipid A moiety and its biological activity in terms of specific ligand-receptor interactions. If lipid A-receptor interaction involves formation of phosphate-ammonium ion-pair(s) with cationic amino-acid residues, the specific mechanism of action was fully consistent with the underlying experimental data. As a consequence, recognition of lipid A variants by an amphipathic binding sequence BHPHB of a host-cell protein receptor might represent the initial and/or rate-determining molecular event of the mechanism of action of lipid A (or endotoxin). The insight into the molecular mechanism of action and the structure of the lipid A-binding pattern have potential implications for rational drug design strategies of endotoxin-neutralizing agents or binding factors.
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Affiliation(s)
- V Frecer
- Department of Biological Sciences, Science Faculty, National University of Singapore, Singapore
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45
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González L, Asensio JL, Ariosa-Alvarez A, Vérez-Bencomo V, Jiménez-Barbero J. Solution conformation and dynamics of the trisaccharide fragments of the O-antigen of Vibrio cholerae O1, serotypes Inaba and Ogawa. Carbohydr Res 1999; 321:88-95. [PMID: 10612004 DOI: 10.1016/s0008-6215(99)00167-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The conformational behavior of the trisaccharide fragments of the Ogawa and Inaba Vibrio cholera serotypes has been studied using NMR and molecular dynamics (MD). The obtained results indicate that there are no significant differences in the major conformation and in the extent of motion of the glycosidic torsions of these molecules. The differences in biological activity are probably not due to conformational effects but to van der Waals and/or hydrogen bonding interactions between the antigens and the biological receptor.
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Affiliation(s)
- L González
- Departamento Química Orgánica Biológica, Instituto Química Orgánica, CSIC, Madrid, Spain
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46
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Gonzalez L, Bernabe M, Espinosa JF, Tejero-Mateo P, Gil-Serrano A, Mantegazza N, Imberty A, Driguez H, Jimenez-Barbero J. Solvent-dependent conformational behaviour of lipochitoligosaccharides related to Nod factors. Carbohydr Res 1999; 318:10-9. [PMID: 10515048 DOI: 10.1016/s0008-6215(99)00082-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The solution conformation of two lipooligosaccharides related to Nod factors or lipochitoligosaccharides have been analysed by 1D and 2D 1H and 13C NMR spectroscopy, molecular mechanics and dynamics calculations. The obtained data indicate that the glycosidic torsion angles have restricted fluctuations, but may adopt a variety of shapes. Remarkably, the relative orientation of the fatty acid chain towards the oligosaccharide backbone is solvent dependent. In water solution, the acyl residue and the oligosaccharide adopt a quasi-parallel orientation for a significant amount of time.
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Affiliation(s)
- L Gonzalez
- Instituto Quimica Orgánica, CSIC, Madrid, Spain
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47
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Conformational analysis of maltoside heteroanalogues using high-quality NOE data and molecular mechanics calculations. Flexibility as a function of the interglycosidic chalcogen atom. Carbohydr Res 1999. [DOI: 10.1016/s0008-6215(99)00011-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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48
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Vinogradov EV, Petersen BO, Thomas-Oates JE, Duus J, Brade H, Holst O. Characterization of a novel branched tetrasaccharide of 3-deoxy-D-manno-oct-2-ulopyranosonic acid. The structure of the carbohydrate backbone of the lipopolysaccharide from Acinetobacter baumannii strain nctc 10303 (atcc 17904). J Biol Chem 1998; 273:28122-31. [PMID: 9774431 DOI: 10.1074/jbc.273.43.28122] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
For the first time, the tetrasaccharide Kdoalpha2-->5Kdoalpha2-->5(Kdoalpha2-->4)Kdo (Kdo is 3-deoxy-D-manno-oct-2-ulopyranosonic acid) has been identified in a bacterial lipopolysaccharide (LPS), i.e. in the core region of LPS from Acinetobacter baumannii NCTC 10303. The LPS was analyzed using compositional analysis, mass spectrometry, and NMR spectroscopy. The disaccharide D-GlcpNbeta1-->6D-GlcpN, phosphorylated at O-1 and O-4', was identified as the carbohydrate backbone of the lipid A. The Kdo tetrasaccharide is attached to O-6' of this disaccharide and is further substituted by short L-rhamnoglycans of varying length and by the disaccharide D-GlcpNAcalpha1-->4D-GlcpNA (GlcpNA, 2-amino-2-deoxy-glucopyranosuronic acid). The core region is not substituted by phosphate residues and represents a novel core type of bacterial LPS. The complete carbohydrate backbone of the LPS is shown in Structure I as follows: where Rha is rhamnose. Except were indicated, monosaccharides possess the D-configuration. Sugars marked with an asterisk are present in non-stoichiometric amounts.
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Affiliation(s)
- E V Vinogradov
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany
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49
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Duca KA, Jordan PC. Comparison of Selectively Polarizable Force Fields for Ion−Water−Peptide Interactions: Ion Translocation in a Gramicidin-like Channel. J Phys Chem B 1998. [DOI: 10.1021/jp981995z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karen A. Duca
- Program in Biophysics and Department of Chemistry, Brandeis University, P.O. Box 9110, Waltham, Massachussetts 02454-9110
| | - Peter C. Jordan
- Program in Biophysics and Department of Chemistry, Brandeis University, P.O. Box 9110, Waltham, Massachussetts 02454-9110
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50
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Beier T, Höltje HD. Modified cyclodextrins as chiral selectors: molecular modelling investigations on the enantioselective binding properties of heptakis(2,3-di-O-methyl-6-O-tert.-butyldimethylsilyl)-beta-cyclodextri n. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1998; 708:1-20. [PMID: 9653941 DOI: 10.1016/s0378-4347(97)00636-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular modelling methods have been used to investigate the enantioselective binding properties of chiral dihydrofuranones on heptakis(2,3-di-O-methyl-6-O-tert.-butyldimethylsilyl)-beta-cyclod extrin in capillary gas chromatography. A conformational analysis of the modified beta-cyclodextrin was performed using annealed molecular dynamics. With the program GRID the molecular interaction potential for each of the received energetically reasonable structures of the beta-cyclodextrin and the dihydrofuranones was evaluated using different probe groups. The results of these computations have been used as starting points for constructing geometrically reasonable host-guest complexes between the beta-cyclodextrin and the dihydrofuranones. The subsequently performed molecular dynamics simulations yielded different complex states reflecting the conformational flexibility of the diastereomeric complexes. Considering the evaluated interaction energy between the beta-cyclodextrin and the dihydrofuranones as a measure of complex stability the results are in close agreement with the experimentally determined elution sequences. The methodology for the construction of the interaction model used in this study is capable of simulating the experimental data. We believe that it may serve as a basis for predictions of hitherto unknown elution sequences at modified cyclodextrins.
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Affiliation(s)
- T Beier
- Institute of Pharmacy, Free University of Berlin, Germany
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