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Curtidor H, Reyes C, Bermúdez A, Vanegas M, Varela Y, Patarroyo ME. Conserved Binding Regions Provide the Clue for Peptide-Based Vaccine Development: A Chemical Perspective. Molecules 2017; 22:molecules22122199. [PMID: 29231862 PMCID: PMC6149789 DOI: 10.3390/molecules22122199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
Synthetic peptides have become invaluable biomedical research and medicinal chemistry tools for studying functional roles, i.e., binding or proteolytic activity, naturally-occurring regions’ immunogenicity in proteins and developing therapeutic agents and vaccines. Synthetic peptides can mimic protein sites; their structure and function can be easily modulated by specific amino acid replacement. They have major advantages, i.e., they are cheap, easily-produced and chemically stable, lack infectious and secondary adverse reactions and can induce immune responses via T- and B-cell epitopes. Our group has previously shown that using synthetic peptides and adopting a functional approach has led to identifying Plasmodium falciparumconserved regions binding to host cells. Conserved high activity binding peptides’ (cHABPs) physicochemical, structural and immunological characteristics have been taken into account for properly modifying and converting them into highly immunogenic, protection-inducing peptides (mHABPs) in the experimental Aotus monkey model. This article describes stereo–electron and topochemical characteristics regarding major histocompatibility complex (MHC)-mHABP-T-cell receptor (TCR) complex formation. Some mHABPs in this complex inducing long-lasting, protective immunity have been named immune protection-inducing protein structures (IMPIPS), forming the subunit components in chemically synthesized vaccines. This manuscript summarizes this particular field and adds our recent findings concerning intramolecular interactions (H-bonds or π-interactions) enabling proper IMPIPS structure as well as the peripheral flanking residues (PFR) to stabilize the MHCII-IMPIPS-TCR interaction, aimed at inducing long-lasting, protective immunological memory.
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Affiliation(s)
- Hernando Curtidor
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- School of Medicine and Health Sciences, University of Rosario, Bogotá 111321, Colombia.
| | - César Reyes
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
| | - Adriana Bermúdez
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- School of Medicine and Health Sciences, University of Rosario, Bogotá 111321, Colombia.
| | - Magnolia Vanegas
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- School of Medicine and Health Sciences, University of Rosario, Bogotá 111321, Colombia.
| | - Yahson Varela
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- Faculty of Health Sciences, Applied and Environmental Sciences University (UDCA), Bogotá 111321, Colombia.
| | - Manuel E Patarroyo
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- Faculty of Medicine, National University of Colombia, Bogotá 111321, Colombia.
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Harmon TS, Holehouse AS, Rosen MK, Pappu RV. Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins. eLife 2017; 6:30294. [PMID: 29091028 PMCID: PMC5703641 DOI: 10.7554/elife.30294] [Citation(s) in RCA: 423] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/29/2017] [Indexed: 01/01/2023] Open
Abstract
Phase transitions of linear multivalent proteins control the reversible formation of many intracellular membraneless bodies. Specific non-covalent crosslinks involving domains/motifs lead to system-spanning networks referred to as gels. Gelation transitions can occur with or without phase separation. In gelation driven by phase separation multivalent proteins and their ligands condense into dense droplets, and gels form within droplets. System spanning networks can also form without a condensation or demixing of proteins into droplets. Gelation driven by phase separation requires lower protein concentrations, and seems to be the biologically preferred mechanism for forming membraneless bodies. Here, we use coarse-grained computer simulations and the theory of associative polymers to uncover the physical properties of intrinsically disordered linkers that determine the extent to which gelation of linear multivalent proteins is driven by phase separation. Our findings are relevant for understanding how sequence-encoded information in disordered linkers influences phase transitions of multivalent proteins. Our cells contain a variety of structures called organelles that perform specific roles within a cell. Some organelles are surrounded by a membrane, while others float inside the cell as spherical droplets made of proteins. These proteins contain several sticky regions, which are connected by flexible linker proteins. It is thought that the level of stickiness and the number of sticky regions, or domains, determine whether a protein will form a membraneless organelle. Often, proteins with similar sticky domains have different linkers, and until now, it was assumed that the linkers do not have any other purpose than stringing the domains together. To test this further, Harmon et al. used a combination of computer simulations and physics-based theory. In these simulations, the domains were kept the same, but the properties of linkers were changed to see if this would influence how the membraneless organelles are formed. The results showed that depending on the physical properties of the linkers, the proteins could huddle together and form dense spherical gel-like droplets similar to the membraneless organelles, or form open non-spherical gels. When the linkers were short, the proteins do not easily form droplets. Linkers that were sufficiently long but too bulky, lead to non-spherical gels. Compact linkers, however, enabled proteins to huddle and form spherical gels. The spherical droplet-spanning gels required much less protein compared to the open non-spherical gels. This suggests that proteins important for forming membraneless organelles can be distinguished from those that are not based on the properties of their linkers – even when their domains are similar. These findings further scientists’ knowledge of how specific types of proteins form membraneless organelles and will help to understand how membraneless organelles control many key aspects of how a cell works.
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Affiliation(s)
- Tyler S Harmon
- Center for Biological Systems Engineering, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, United States
| | - Alex S Holehouse
- Center for Biological Systems Engineering, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, United States
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, United States
| | - Rohit V Pappu
- Center for Biological Systems Engineering, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, United States
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Chalyavi F, Hogle DG, Tucker MJ. Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics. J Phys Chem B 2017; 121:6380-6389. [DOI: 10.1021/acs.jpcb.7b04999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - David G. Hogle
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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54
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Rajeshwar T R, Krishnan M. Direct Determination of Site-Specific Noncovalent Interaction Strengths of Proteins from NMR-Derived Fast Side Chain Motional Parameters. J Phys Chem B 2017; 121:5174-5186. [PMID: 28452484 DOI: 10.1021/acs.jpcb.7b01402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel approach to accurately determine residue-specific noncovalent interaction strengths (ξ) of proteins from NMR-measured fast side chain motional parameters (Oaxis2) is presented. By probing the environmental sensitivity of side chain conformational energy surfaces of individual residues of a diverse set of proteins, the microscopic connections between ξ, Oaxis2, conformational entropy (Sconf), conformational barriers, and rotamer stabilities established here are found to be universal among proteins. The results reveal that side chain flexibility and conformational entropy of each residue decrease with increasing ξ and that for each residue type there exists a critical range of ξ, determined primarily by the mean side chain conformational barriers, within which flexibility of any residue can be reversibly tuned from highly flexible (with Oaxis2 ∼ 0) to highly restricted (with Oaxis2 ∼ 1) by increasing ξ by ∼3 kcal/mol. Beyond this critical range of ξ, both side chain flexibility and conformational entropy are insensitive to ξ. The interrelationships between conformational dynamics, conformational entropy, and noncovalent interactions of protein side chains established here open up new avenues to probe perturbation-induced (for example, ligand-binding, temperature, pressure) changes in fast side chain dynamics and thermodynamics of proteins by comparing their conformational energy surfaces in the native and perturbed states.
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Affiliation(s)
- Rajitha Rajeshwar T
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Gachibowli, Hyderabad 500 032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Gachibowli, Hyderabad 500 032, India
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Giełdoń A, Witt MM, Gajewicz A, Puzyn T. Rapid insight into C60 influence on biological functions of proteins. Struct Chem 2017. [DOI: 10.1007/s11224-017-0957-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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56
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Xu ZX, Ma GL, Zhang Q, Chen CH, He YM, Xu LH, Zhou GR, Li ZH, Yang HJ, Zhou P. Inhibitory Mechanism of Epigallocatechin Gallate on Fibrillation and Aggregation of Amidated Human Islet Amyloid Polypeptide. Chemphyschem 2017; 18:1611-1619. [PMID: 28297133 DOI: 10.1002/cphc.201700057] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 01/06/2023]
Abstract
The abnormal fibrillation of human islet amyloid polypeptide (hIAPP) is associated with development of type II diabetes mellitus (T2DM). (-)-Epigallocatechin gallate (EGCG) can bind amyloid proteins to inhibit the fibrillation of these proteins. However, the mechanic detail of EGCG inhibiting amyloid formation is still unclear at the molecular level. In the present work, we sought to investigate the effect of EGCG on amidated hIAPP (hIAPP-NH2 ) fibrillation and aggregation by using spectroscopic and microscopic techniques, and also sought to gain insights into the interaction of EGCG and hIAPP22-27 by using spectroscopic experiments and quantum chemical calculations. ThT fluorescence, real-time NMR, and TEM studies demonstrated that EGCG inhibits the formation of hIAPP-NH2 fibrils, while promoting the formation of hIAPP-NH2 amorphous aggregates. Phenylalanine intrinsic fluorescence and NMR studies of the EGCG/hIAPP22-27 complex revealed three important binding sites including the A ring of EGCG, residue Phe23, and residue Ile26. DFT calculations identified the dominant binding structures of EGCG/Phe23 and EGCG/Ile26 complexes, named structure I and structure II, respectively. Our study demonstrates the inhibitory mechanism of EGCG on fibrillation and aggregation of hIAPP-NH2 in which EGCG interacts with hIAPP-NH2 through hydrogen bonding and π-π interactions between the A ring and residue Phe23 as well as hydrophobic interactions between the A ring and residue Ile26, which can thus inhibit the interpeptide interaction between hIAPP-NH2 monomers and finally inhibit fibrillation of hIAPP-NH2 . This study agrees with and reinforces previous studies and offers an intuitive explanation at both the atomic and molecular levels. Our findings may provide an invaluable reference for the future development of new drugs in the management of diabetes.
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Affiliation(s)
- Zhi-Xue Xu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
| | - Gong-Li Ma
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Qiang Zhang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, P. R. China
| | - Cong-Heng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
| | - Yan-Ming He
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, P. R. China
| | - Li-Hui Xu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
| | - Guang-Rong Zhou
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
| | - Zhen-Hua Li
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Hong-Jie Yang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, P. R. China
| | - Ping Zhou
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
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57
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Esrafili MD, Sadr-Mousavi A. Modulating of the pnicogen-bonding by a H⋯π interaction: An ab initio study. J Mol Graph Model 2017; 75:165-173. [PMID: 28595167 DOI: 10.1016/j.jmgm.2017.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 11/29/2022]
Abstract
An ab initio study of the cooperativity in XH2P⋯NCH⋯Z and XH2P⋯CNH⋯Z complexes (X=F, Cl, Br, CN, NC; Z=C2H2,C6H6) connected by pnicogen-bonding and H⋯π interactions is carried out by means of MP2 computational method. A detailed analysis of the structures, interaction energies and bonding properties is performed on these systems. For each set of the complexes considered, a favorable cooperativity is observed, especially in X=F and CN complexes. However, for a given X or Z, the amount of cooperativity effects in XH2P⋯CNH⋯Z complexes are more important than XH2P⋯NCH⋯Z counterparts. Besides, the influence of a H⋯π interaction on a P⋯N (C) bond is more pronounced than that of a P⋯N (C) bond on a H⋯π bond. The quantum theory of atoms in molecules shows that ternary complexes have increased electron densities at their bond critical points relative to the corresponding binary systems. The results also indicate that the strength of the P⋯N(C) and H⋯π interactions increases in the presence of the solvent.
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Affiliation(s)
- Mehdi D Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, P.O. Box: 5513864596, Maragheh, Iran.
| | - Asma Sadr-Mousavi
- School of Chemistry, University College of Science, University of Tehran, Tehran, Iran
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58
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González-Rosende ME, Castillo E, Jennings WB, Malone JF. Stereodynamics and edge-to-face CH-π aromatic interactions in imino compounds containing heterocyclic rings. Org Biomol Chem 2017; 15:1484-1494. [PMID: 28116383 DOI: 10.1039/c6ob02618d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By comparison with close contact interactions between benzene rings there is a paucity of experimental data available for attractive interactions involving aromatic heterocyclic rings, especially for small molecules in solution. Herein we describe aromatic heterocyclic and carbocyclic edge-to face interactions and conformational stereodynamics of N-1,2-diphenylethyl imines bearing a phenyl group and either a 2-pyridyl, 3-pyridyl, 2-thiophene or 2-furanyl moiety on the imino carbon. X-ray crystal structures have been determined for two compounds. Slow rotation about the phenyl-imino bond in the E-isomers and around the heterocycle-imino bond in the Z-isomers of the pyridyl compounds was observed at low temperatures by NMR. Abnormally large shielding of one ortho hydrogen indicates that both the imino phenyl and heterocycle rings can engage in an edge-to-face interaction with the N-terminal phenyl moiety in the appropriate isomer. Some rotational barriers around the phenyl-imino and heterocycle-imino bonds were measured.
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Affiliation(s)
- M Eugenia González-Rosende
- Departamento de Farmacia, Universidad CEU Cardenal Herrera, Avda. Seminario s/n, 46113, Moncada, Valencia, Spain.
| | - Encarna Castillo
- Departamento de Farmacia, Universidad CEU Cardenal Herrera, Avda. Seminario s/n, 46113, Moncada, Valencia, Spain.
| | - W Brian Jennings
- Department of Chemistry and Analytical & Biological Chemistry Research Facility, University College Cork, Cork, Ireland.
| | - John F Malone
- School of Chemistry & Chemical Engineering, The Queen's University of Belfast, Belfast BT9 5AG, UK
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59
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Akher FB, Ebrahimi A, Mostafavi N. Characterization of π-stacking interactions between aromatic amino acids and quercetagetin. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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60
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Zhang W, Yang H, Liu F, Chen T, Hu G, Guo D, Hou Q, Wu X, Su Y, Wang J. Molecular interactions between DOPA and surfaces with different functional groups: a chemical force microscopy study. RSC Adv 2017. [DOI: 10.1039/c7ra04228k] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The adhesion of mussel foot proteins (Mfps) to a variety of surfaces has been widely investigated, but the mechanisms behind the mussel adhesion to surfaces with different properties are far from being understood.
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61
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El Hage K, Pandyarajan V, Phillips NB, Smith BJ, Menting JG, Whittaker J, Lawrence MC, Meuwly M, Weiss MA. Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY. J Biol Chem 2016; 291:27023-27041. [PMID: 27875310 PMCID: PMC5207135 DOI: 10.1074/jbc.m116.761015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/31/2016] [Indexed: 12/13/2022] Open
Abstract
Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (TyrB26) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-TyrB26]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (TyrB16, PheB24, PheB25, 3-I-TyrB26, and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-TyrB26]insulin analog (determined as an R6 zinc hexamer). Given that residues B24-B30 detach from the core on receptor binding, the environment of 3-I-TyrB26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a "micro-receptor" complex, we predict that 3-I-TyrB26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such "halogen engineering" promises to extend principles of medicinal chemistry to proteins.
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Affiliation(s)
- Krystel El Hage
- From the Department of Chemistry, University of Basel, Klingelbergstrasse 80 CH-4056 Basel, Switzerland
| | | | | | - Brian J Smith
- the La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - John G Menting
- the The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, and
| | | | - Michael C Lawrence
- the The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, and
- the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Markus Meuwly
- From the Department of Chemistry, University of Basel, Klingelbergstrasse 80 CH-4056 Basel, Switzerland,
| | - Michael A Weiss
- the Departments of Biochemistry,
- Medicine, and
- Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106
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Hwang JW, Li P, Shimizu KD. Synergy between experimental and computational studies of aromatic stacking interactions. Org Biomol Chem 2016; 15:1554-1564. [PMID: 27878156 DOI: 10.1039/c6ob01985d] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aromatic stacking interactions are one of the most common types of non-covalent interactions. However, their fundamental origins and the ability to accurately predict their stability trends are still an active area of research. The study of aromatic stacking interactions has been particularly challenging. The interaction involves a delicate balance of multiple forces, and the aromatic surfaces can readily adopt different interaction geometries. Thus, the collaborative efforts of theoretical and experimental researchers have been essential to understand and build more accurate predictive models of aromatic stacking interactions.
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Affiliation(s)
- Jung Wun Hwang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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63
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Petrov A, Arzhanik V, Makarov G, Koliasnikov O. A novel Arg H52/Tyr H33 conservative motif in antibodies: A correlation between sequence of antibodies and antigen binding. J Bioinform Comput Biol 2016; 14:1650019. [PMID: 27452033 DOI: 10.1142/s0219720016500190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antibodies are the family of proteins, which are responsible for antigen recognition. The computational modeling of interaction between an antigen and an antibody is very important when crystallographic structure is unavailable. In this research, we have discovered the correlation between the amino acid sequence of antibody and its specific binding characteristics on the example of the novel conservative binding motif, which consists of four residues: Arg H52, Tyr H33, Thr H59, and Glu H61. These residues are specifically oriented in the binding site and interact with each other in a specific manner. The residues of the binding motif are involved in interaction strictly with negatively charged groups of antigens, and form a binding complex. Mechanism of interaction and characteristics of the complex were also discovered. The results of this research can be used to increase the accuracy of computational antibody-antigen interaction modeling and for post-modeling quality control of the modeled structures.
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Affiliation(s)
- Artem Petrov
- * Kolmogorov Advanced Educational Scientific Center, Lomonosov Moscow State University, Kremenchugskaya st., 11, Moscow, 121357, Russia
| | - Vladimir Arzhanik
- † Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, LenGory, 1, b.73, Moscow, 119991, Russia
| | - Gennady Makarov
- ‡ Department of Chemistry, Lomonosov Moscow State University, LenGory, 1, b.3, Moscow, 119991, Russia
| | - Oleg Koliasnikov
- * Kolmogorov Advanced Educational Scientific Center, Lomonosov Moscow State University, Kremenchugskaya st., 11, Moscow, 121357, Russia
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Synthesis, characterization and biological application of four novel metal-Schiff base complexes derived from allylamine and their interactions with human serum albumin: Experimental, molecular docking and ONIOM computational study. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:448-462. [PMID: 27450299 DOI: 10.1016/j.jphotobiol.2016.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/02/2016] [Indexed: 12/20/2022]
Abstract
Novel metal-based drug candidate including VOL2, NiL2, CuL2 and PdL2 have been synthesized from 2-hydroxy-1-allyliminomethyl-naphthalen ligand and have been characterized by means of elemental analysis (CHN), FT-IR and UV-vis spectroscopies. In addition, (1)H and (13)C NMR techniques were employed for characterization of the PdL2 complex. Single-crystal X-ray diffraction technique was utilized to characterise the structure of the complexes. The Cu(II), Ni(II) and Pd(II) complexes show a square planar trans-coordination geometry, while in the VOL2, the vanadium center has a distorted tetragonal pyramidal N2O3 coordination sphere. The HSA-binding was also determined, using fluorescence quenching, UV-vis spectroscopy, and circular dichroism (CD) titration method. The obtained results revealed that the HSA affinity for binding the synthesized compounds follows as PdL2>CuL2>VOL2>NiL2, indicating the effect of metal ion on binding constant. The distance between these compounds and HSA was obtained based on the Förster's theory of non-radiative energy transfer. Furthermore, computational methods including molecular docking and our Own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) were carried out to investigate the HSA-binding of the compounds. Molecular docking calculation indicated the existence of hydrogen bond between amino acid residues of HSA and all synthesized compounds. The formation of the hydrogen bond in the HSA-compound systems leads to their stabilization. The ONIOM method was utilized in order to investigate HSA binding of compounds more precisely in which molecular mechanics method (UFF) and semi empirical method (PM6) were selected for the low layer and the high layer, respectively. The results show that the structural parameters of the compounds changed along with binding to HSA, indicating the strong interaction between the compounds and HSA. The value of binding constant depends on the extent of the resultant changes. This should be mentioned that both theoretical methods calculated the Kb values in the same sequence and are in a good agreement with the experimental data.
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66
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Pandyarajan V, Phillips NB, Rege N, Lawrence MC, Whittaker J, Weiss MA. Contribution of TyrB26 to the Function and Stability of Insulin: STRUCTURE-ACTIVITY RELATIONSHIPS AT A CONSERVED HORMONE-RECEPTOR INTERFACE. J Biol Chem 2016; 291:12978-90. [PMID: 27129279 DOI: 10.1074/jbc.m115.708347] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 11/06/2022] Open
Abstract
Crystallographic studies of insulin bound to receptor domains have defined the primary hormone-receptor interface. We investigated the role of Tyr(B26), a conserved aromatic residue at this interface. To probe the evolutionary basis for such conservation, we constructed 18 variants at B26. Surprisingly, non-aromatic polar or charged side chains (such as Glu, Ser, or ornithine (Orn)) conferred high activity, whereas the weakest-binding analogs contained Val, Ile, and Leu substitutions. Modeling of variant complexes suggested that the B26 side chains pack within a shallow depression at the solvent-exposed periphery of the interface. This interface would disfavor large aliphatic side chains. The analogs with highest activity exhibited reduced thermodynamic stability and heightened susceptibility to fibrillation. Perturbed self-assembly was also demonstrated in studies of the charged variants (Orn and Glu); indeed, the Glu(B26) analog exhibited aberrant aggregation in either the presence or absence of zinc ions. Thus, although Tyr(B26) is part of insulin's receptor-binding surface, our results suggest that its conservation has been enjoined by the aromatic ring's contributions to native stability and self-assembly. We envisage that such classical structural relationships reflect the implicit threat of toxic misfolding (rather than hormonal function at the receptor level) as a general evolutionary determinant of extant protein sequences.
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Affiliation(s)
| | | | | | - Michael C Lawrence
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Michael A Weiss
- From the Departments of Biochemistry, Medicine, and Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106,
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68
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Koyano H, Hayashida M, Akutsu T. Maximum margin classifier working in a set of strings. Proc Math Phys Eng Sci 2016; 472:20150551. [PMID: 27118908 PMCID: PMC4841474 DOI: 10.1098/rspa.2015.0551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/02/2016] [Indexed: 11/12/2022] Open
Abstract
Numbers and numerical vectors account for a large portion of data. However, recently, the amount of string data generated has increased dramatically. Consequently, classifying string data is a common problem in many fields. The most widely used approach to this problem is to convert strings into numerical vectors using string kernels and subsequently apply a support vector machine that works in a numerical vector space. However, this non-one-to-one conversion involves a loss of information and makes it impossible to evaluate, using probability theory, the generalization error of a learning machine, considering that the given data to train and test the machine are strings generated according to probability laws. In this study, we approach this classification problem by constructing a classifier that works in a set of strings. To evaluate the generalization error of such a classifier theoretically, probability theory for strings is required. Therefore, we first extend a limit theorem for a consensus sequence of strings demonstrated by one of the authors and co-workers in a previous study. Using the obtained result, we then demonstrate that our learning machine classifies strings in an asymptotically optimal manner. Furthermore, we demonstrate the usefulness of our machine in practical data analysis by applying it to predicting protein-protein interactions using amino acid sequences and classifying RNAs by the secondary structure using nucleotide sequences.
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Affiliation(s)
- Hitoshi Koyano
- Laboratory of Biostatistics and Bioinformatics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Morihiro Hayashida
- Laboratory of Mathematical Bioinformatics, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Tatsuya Akutsu
- Laboratory of Mathematical Bioinformatics, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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69
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Gunio D, Froehlig J, Pappas K, Ferguson U, Wade H. Solution-Binding and Molecular Docking Approaches Combine to Provide an Expanded View of Multidrug Recognition in the MDR Gene Regulator BmrR. J Chem Inf Model 2016; 56:377-89. [DOI: 10.1021/acs.jcim.5b00704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Drew Gunio
- Department
of Biophysics
and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, United States
| | - John Froehlig
- Department
of Biophysics
and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, United States
| | - Katerina Pappas
- Department
of Biophysics
and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, United States
| | - Uneeke Ferguson
- Department
of Biophysics
and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, United States
| | - Herschel Wade
- Department
of Biophysics
and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, United States
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70
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Kulkarni GS, Reddy K, Zang W, Lee K, Fan X, Zhong Z. Electrical Probing and Tuning of Molecular Physisorption on Graphene. NANO LETTERS 2016; 16:695-700. [PMID: 26709716 DOI: 10.1021/acs.nanolett.5b04500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ability to tune the molecular interaction electronically can have profound impact on wide-ranging scientific frontiers in catalysis, chemical and biological sensor development, and the understanding of key biological processes. Despite that electrochemistry is routinely used to probe redox reactions involving loss or gain of electrons, electrical probing and tuning of the weaker noncovalent interactions, such as molecular physisorption, have been challenging, primarily due to the inability to change the work function of conventional metal electrodes. To this end, we report electrical probing and tuning of the noncovalent physisorption of polar molecules on graphene surface by using graphene nanoelectronic heterodyne sensors. Temperature-dependent molecular desorptions for six different polar molecules were measured in real-time to study the desorption kinetics and extract the binding affinities. More importantly, we demonstrate electrical tuning of molecule-graphene binding kinetics through electrostatic gating of graphene; the molecular desorption can be slowed down nearly three times within a gate voltage range of 15 V. Our results provide insight into small molecule-nanomaterial interaction dynamics and signify the ability to electrically tailor interactions, which can lead to rational designs of complex chemical processes for catalysis and drug discovery.
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Affiliation(s)
- Girish S Kulkarni
- Department of Electrical Engineering and Computer Science, University of Michigan , 1301 Beal Avenue, Ann Arbor, Michigan 48109, United States
| | - Karthik Reddy
- Department of Electrical Engineering and Computer Science, University of Michigan , 1301 Beal Avenue, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan , 1101 Beal Avenue, Ann Arbor, Michigan 48109, United States
| | - Wenzhe Zang
- Department of Electrical Engineering and Computer Science, University of Michigan , 1301 Beal Avenue, Ann Arbor, Michigan 48109, United States
| | - Kyunghoon Lee
- Department of Electrical Engineering and Computer Science, University of Michigan , 1301 Beal Avenue, Ann Arbor, Michigan 48109, United States
| | - Xudong Fan
- Department of Biomedical Engineering, University of Michigan , 1101 Beal Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhaohui Zhong
- Department of Electrical Engineering and Computer Science, University of Michigan , 1301 Beal Avenue, Ann Arbor, Michigan 48109, United States
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71
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The tRNA Elbow in Structure, Recognition and Evolution. Life (Basel) 2016; 6:life6010003. [PMID: 26771646 PMCID: PMC4810234 DOI: 10.3390/life6010003] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 01/07/2023] Open
Abstract
Prominent in the L-shaped three-dimensional structure of tRNAs is the "elbow" where their two orthogonal helical stacks meet. It has a conserved structure arising from the interaction of the terminal loops of the D- and T-stem-loops, and presents to solution a flat face of a tertiary base pair between the D- and T-loops. In addition to the ribosome, which interacts with the elbow in all three of its tRNA binding sites, several cellular RNAs and many proteins are known to recognize the elbow. At least three classes of non-coding RNAs, namely 23S rRNA, ribonuclease P, and the T-box riboswitches, recognize the tRNA elbow employing an identical structural motif consisting of two interdigitated T-loops. In contrast, structural solutions to tRNA-elbow recognition by proteins are varied. Some enzymes responsible for post-transcriptional tRNA modification even disrupt the elbow structure in order to access their substrate nucleotides. The evolutionary origin of the elbow is mysterious, but, because it does not explicitly participate in the flow of genetic information, it has been proposed to be a late innovation. Regardless, it is biologically essential. Even some viruses that hijack the cellular machinery using tRNA decoys have convergently evolved near-perfect mimics of the tRNA elbow.
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72
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Gangele K, Poluri KM. Imidazole derivatives differentially destabilize the low pH conformation of lysozyme through weak electrostatic interactions. RSC Adv 2016. [DOI: 10.1039/c6ra23031h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Imidazole derivatives forms charge transfer complexes with lysozyme at low pH (4–2) and destabilize its conformation through weak electrostatic interactions.
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Affiliation(s)
- Krishnakant Gangele
- Department of Biotechnology
- Indian Institute of Technology Roorkee
- Roorkee – 247667
- India
| | - Krishna Mohan Poluri
- Department of Biotechnology
- Indian Institute of Technology Roorkee
- Roorkee – 247667
- India
- Centre for Nanotechnology
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73
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Marín-Luna M, Alkorta I, Elguero J, Mó O, Yáñez M. Fullerene and corannulene derivatives acting as insulators of Cl−and BeH2. Phys Chem Chem Phys 2016; 18:6059-68. [DOI: 10.1039/c5cp08046k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Corannulene and its benzo-derivatives CxH10(x= 20–60) as prototypes of non-planar π-aromatic systems have been studied as insulators of BeH2and Cl−.
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Affiliation(s)
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC)
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica (CSIC)
- E-28006 Madrid
- Spain
| | - Otilia Mó
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - Manuel Yáñez
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
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74
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Abstract
The role of π-π interactions in controlling the reactivity and selectivity of a chemical reaction is only recently being explored, even though their ubiquitous role in the structural aspects is well known. We have studied Bergman cyclisation focusing on the effect of π-π interactions on the activation barrier and the variation of π-π interactions along the reaction coordinate. We used enediyne substrates that contain phenyl groups connected to the reaction centres (C1 and C6 atoms), separated by 0, 1 and 2 linker groups. The main difference between the substrates is that the Ph groups enjoy different flexibility to accommodate the changes occurring during the progress of the reaction. The path length of the minimum energy path is increased - shortest in the least flexible substrate (a) and longer in the more flexible ones (c, d and e). We calculated the interaction between the Ph groups, the π-π interaction, using BP86-D3BJ, B3LYP-D3BJ, M06-2X, B2PLYP-D3BJ, SCS-MP2, and SAPT. The BP86-D3BJ was found to be sufficiently accurate with a mean absolute deviation of 0.26 kcal mol(-1) with respect to the SAPT2+3 values. The variation in the π-π interaction shows different behaviour in a-e, and this can be correlated with the flexibility of the Ph groups to orient themselves to maintain the optimal relative orientation while conforming to the changes in the reaction coordinate. We analysed the relative orientation of the phenyl groups using certain geometric parameters that showed that when Ph groups can attain a relative orientation close to that of the free dimer, the interaction is maximum. Energy decomposition analysis using SAPT showed that the dispersive interaction is the major contributor (50-60%) to the attractive forces. The π-π interactions influenced the overall activation energy, either by destabilising the substrates or by stabilising the TS - resulting in a variation of about 3.5 kcal mol(-1) in activation energies in a-e. The effect of substituents of different electronic nature was assessed which showed that electron donating and electron withdrawing substituents increase the π-π interactions; however, the TS is more stabilised and hence activation energies are increased.
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Affiliation(s)
- Saibal Jana
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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75
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Mutations in the linker domain affect phospho-STAT3 function and suggest targets for interrupting STAT3 activity. Proc Natl Acad Sci U S A 2015; 112:14811-6. [PMID: 26553978 DOI: 10.1073/pnas.1515876112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Crystallography of the cores of phosphotyrosine-activated dimers of STAT1 (132-713) and STAT3 (127-722) bound to a similar double-stranded deoxyoligonucleotide established the domain structure of the STATs and the structural basis for activation through tyrosine phosphorylation and dimerization. We reported earlier that mutants in the linker domain of STAT1 that connect the DNA-binding domain and SH2 domain can prevent transcriptional activation. Because of the pervasive importance of persistently activated STAT3 in many human cancers and the difficulty of finding useful drug candidates aimed at disrupting the pY interchange in active STAT3 dimers, we have examined effects of an array of mutants in the STAT3 linker domain. We have found several STAT3 linker domain mutants to have profound effects of inhibiting STAT3 transcriptional activation. From these results, we propose (i) there is definite functional interaction of the linker both with the DNA binding domain and with the SH2 domain, and (ii) these putative contacts provide potential new targets for small molecule-induced pSTAT3 inhibition.
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76
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Conformational Preferences of π–π Stacking Between Ligand and Protein, Analysis Derived from Crystal Structure Data Geometric Preference of π–π Interaction. Interdiscip Sci 2015; 7:211-20. [DOI: 10.1007/s12539-015-0263-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 04/01/2014] [Accepted: 06/03/2015] [Indexed: 10/23/2022]
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77
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Venugopalan P, Kishore R. Antiparallel Self-Association of a γ,α-Hybrid Peptide: More Relevance of Weak Interactions. Chem Asian J 2015; 10:1753-60. [PMID: 25965414 DOI: 10.1002/asia.201500373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Indexed: 11/08/2022]
Abstract
To learn how a preorganized peptide-based molecular template, together with diverse weak non-covalent interactions, leads to an effective self-association, we investigated the conformational characteristics of a simple γ,α-hybrid model peptide, Boc-γ-Abz-Gly-OMe. The single-crystal X-ray diffraction analysis revealed the existence of a fully extended β-strand-like structure stabilized by two non-conventional C-H⋅⋅⋅O=C intramolecular H-bonds. The 2D (1) H NMR ROESY experiment led us to propose that the flat topology of the urethane-γ-Abz-amide moiety is predominantly preserved in a non-polar environment. The self-association of the energetically more favorable antiparallel β-strand-mimic in solid-state engenders an unusual 'flight of stairs' fabricated through face-to-face and edge-to-edge Ar⋅⋅⋅Ar interactions. In conjunction with FT-IR spectroscopic analysis in chloroform, we highlight that conformationally semi-rigid γ-Abz foldamer in appositely designed peptides may encourage unusual β-strand or β-sheet-like self-association and supramolecular organization stabilized via weak attractive forces.
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Affiliation(s)
- Paloth Venugopalan
- Department of Chemistry, Panjab University, Sector 14, Chandigarh-, 160 014, India
| | - Raghuvansh Kishore
- Protein Science & Engineering Division, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh-, 160 036, India.
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78
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Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
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79
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Frauenkron-Machedjou VJ, Fulton A, Zhu L, Anker C, Bocola M, Jaeger KE, Schwaneberg U. Towards Understanding Directed Evolution: More than Half of All Amino Acid Positions Contribute to Ionic Liquid Resistance ofBacillus subtilisLipase A. Chembiochem 2015; 16:937-45. [DOI: 10.1002/cbic.201402682] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 01/17/2023]
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80
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The stacking geometries and association thermodynamics of oxalyl acid N,N ′-dibenzoyl-hydrazide derivatives studied by NMR. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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81
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Hussain HB, Wilson KA, Wetmore SD. Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur. Aust J Chem 2015. [DOI: 10.1071/ch14598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
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82
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Irie M, Fukaminato T, Matsuda K, Kobatake S. Photochromism of Diarylethene Molecules and Crystals: Memories, Switches, and Actuators. Chem Rev 2014; 114:12174-277. [DOI: 10.1021/cr500249p] [Citation(s) in RCA: 1755] [Impact Index Per Article: 175.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Masahiro Irie
- Research
Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Tuyoshi Fukaminato
- Research
Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku,
Sapporo 001-0020, Japan
| | - Kenji Matsuda
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Seiya Kobatake
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka 558-8585, Japan
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83
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Toward understanding driving forces in membrane protein folding. Arch Biochem Biophys 2014; 564:297-313. [DOI: 10.1016/j.abb.2014.07.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
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84
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Celandroni F, Salvetti S, Senesi S, Ghelardi E. Bacillus thuringiensis membrane-damaging toxins acting on mammalian cells. FEMS Microbiol Lett 2014; 361:95-103. [PMID: 25283838 DOI: 10.1111/1574-6968.12615] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 01/20/2023] Open
Abstract
Bacillus thuringiensis is widely used as a biopesticide in forestry and agriculture, being able to produce potent species-specific insecticidal toxins and considered nonpathogenic to other animals. More recently, however, repeated observations are documenting the association of this microorganism with various infectious diseases in humans, such as food-poisoning-associated diarrheas, periodontitis, bacteremia, as well as ocular, burn, and wound infections. Similar to B. cereus, B. thuringiensis produces an array of virulence factors acting against mammalian cells, such as phosphatidylcholine- and phosphatidylinositol-specific phospholipase C (PC-PLC and PI-PLC), hemolysins, in particular hemolysin BL (HBL), and various enterotoxins. The contribution of some of these toxins to B. thuringiensis pathogenicity has been studied in animal models of infection, following intravitreous, intranasal, or intratracheal inoculation. These studies lead to the speculation that the activities of PC-PLC, PI-PLC, and HBL are responsible for most of the pathogenic properties of B. thuringiensis in nongastrointestinal infections in mammals. This review summarizes data regarding the biological activity, the genetic basis, and the structural features of these membrane-damaging toxins.
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Affiliation(s)
- Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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85
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Pandyarajan V, Smith BJ, Phillips NB, Whittaker L, Cox GP, Wickramasinghe N, Menting JG, Wan ZL, Whittaker J, Ismail-Beigi F, Lawrence MC, Weiss MA. Aromatic anchor at an invariant hormone-receptor interface: function of insulin residue B24 with application to protein design. J Biol Chem 2014; 289:34709-27. [PMID: 25305014 DOI: 10.1074/jbc.m114.608562] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Crystallographic studies of insulin bound to fragments of the insulin receptor have recently defined the topography of the primary hormone-receptor interface. Here, we have investigated the role of Phe(B24), an invariant aromatic anchor at this interface and site of a human mutation causing diabetes mellitus. An extensive set of B24 substitutions has been constructed and tested for effects on receptor binding. Although aromaticity has long been considered a key requirement at this position, Met(B24) was found to confer essentially native affinity and bioactivity. Molecular modeling suggests that this linear side chain can serve as an alternative hydrophobic anchor at the hormone-receptor interface. These findings motivated further substitution of Phe(B24) by cyclohexanylalanine (Cha), which contains a nonplanar aliphatic ring. Contrary to expectations, [Cha(B24)]insulin likewise exhibited high activity. Furthermore, its resistance to fibrillation and the rapid rate of hexamer disassembly, properties of potential therapeutic advantage, were enhanced. The crystal structure of the Cha(B24) analog, determined as an R6 zinc-stabilized hexamer at a resolution of 1.5 Å, closely resembles that of wild-type insulin. The nonplanar aliphatic ring exhibits two chair conformations with partial occupancies, each recapitulating the role of Phe(B24) at the dimer interface. Together, these studies have defined structural requirements of an anchor residue within the B24-binding pocket of the insulin receptor; similar molecular principles are likely to pertain to insulin-related growth factors. Our results highlight in particular the utility of nonaromatic side chains as probes of the B24 pocket and suggest that the nonstandard Cha side chain may have therapeutic utility.
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Affiliation(s)
| | - Brian J Smith
- the La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | | | | | | | | | - John G Menting
- the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, and
| | | | | | | | - Michael C Lawrence
- the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, and the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael A Weiss
- From the Departments of Biochemistry, Medicine, and Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106,
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86
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Amtul Z, Rahman AU. Neural Plasticity and Memory: Is Memory Encoded in Hydrogen Bonding Patterns? Neuroscientist 2014; 22:9-18. [PMID: 25168338 DOI: 10.1177/1073858414547934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Current models of memory storage recognize posttranslational modification vital for short-term and mRNA translation for long-lasting information storage. However, at the molecular level things are quite vague. A comprehensive review of the molecular basis of short and long-lasting synaptic plasticity literature leads us to propose that the hydrogen bonding pattern at the molecular level may be a permissive, vital step of memory storage. Therefore, we propose that the pattern of hydrogen bonding network of biomolecules (glycoproteins and/or DNA template, for instance) at the synapse is the critical edifying mechanism essential for short- and long-term memories. A novel aspect of this model is that nonrandom impulsive (or unplanned) synaptic activity functions as a synchronized positive-feedback rehearsal mechanism by revising the configurations of the hydrogen bonding network by tweaking the earlier tailored hydrogen bonds. This process may also maintain the elasticity of the related synapses involved in memory storage, a characteristic needed for such networks to alter intricacy and revise endlessly. The primary purpose of this review is to stimulate the efforts to elaborate the mechanism of neuronal connectivity both at molecular and chemical levels.
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Affiliation(s)
- Zareen Amtul
- Department of Psychiatry, University of Western Ontario, London, Ontario, Canada H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Atta-Ur Rahman
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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87
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Wani NA, Gupta VK, Kant R, Aravinda S, Rai R. An unusual conformation of gabapentin (Gpn) in Pyr-Gpn-NH-NH-Pyr stabilized by weak interactions. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2014; 70:776-9. [PMID: 25093358 DOI: 10.1107/s2053229614015587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/03/2014] [Indexed: 11/10/2022]
Abstract
The crystal structure of N-[(1-{2-oxo-2-[2-(pyrazin-2-ylcarbonyl)hydrazin-1-yl]ethyl}cyclohexyl)methyl]pyrazine-2-carboxamide monohydrate (Pyr-Gpn-NN-NH-Pyr·H2O), C19H23N7O3·H2O, reveals an unusual trans-gauche (tg(-)) conformation for the gabapentin (Gpn) residue around the C(γ)-C(β) (θ1) and C(β)-C(α) (θ2) bonds. The molecular conformation is stabilized by intramolecular N-H...N hydrogen bonds and weak C-H...O interactions. The packing of the molecules in the crystal lattice shows a network of strong N-H...O and O-H...O hydrogen bonds together with weak C-H...O and π-π inteactions.
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Affiliation(s)
- Naiem Ahmad Wani
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180 001, India
| | - Vivek Kumar Gupta
- X-ray Crystallography Laboratory, Post-Graduate Department of Physics & Electronics, University of Jammu, Jammu Tawi 180 006, India
| | - Rajni Kant
- X-ray Crystallography Laboratory, Post-Graduate Department of Physics & Electronics, University of Jammu, Jammu Tawi 180 006, India
| | - Subrayashastry Aravinda
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180 001, India
| | - Rajkishor Rai
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180 001, India
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88
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Kobayashi Y, Tsutsumi H, Abe T, Ikeda K, Tashiro Y, Unzai S, Kamikubo H, Kataoka M, Hiroaki H, Hamada D. Decreased amyloidogenicity caused by mutational modulation of surface properties of the immunoglobulin light chain BRE variable domain. Biochemistry 2014; 53:5162-73. [PMID: 25062800 DOI: 10.1021/bi5007892] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Amyloid formation by immunoglobulin light chain (LC) proteins is associated with amyloid light chain (AL) amyloidosis. Destabilization of the native state of the variable domain of the LC (VL) is known to be one of the critical factors in promoting the formation of amyloid fibrils. However, determining the key residues involved in this destabilization remains challenging, because of the existence of a number of intrinsic sequence variations within VL. In this study, we identified the key residues for destabilization of the native state of amyloidogenic VL in the LC of BRE by analyzing the stability of chimeric mutants of BRE and REI VL; the latter immunoglobulin is not associated with AL amyloidosis. The results suggest that the surface-exposed residues N45 and D50 are the key residues in the destabilization of the native state of BRE VL. Point mutations at the corresponding residues in REI VL (K45N, E50D, and K45N/E50D) destabilized the native state and increased amyloidogenicity. However, the reverse mutations in BRE VL (N45K, D50E, and N45K/D50E) re-established the native state and decreased amyloidogenicity. Thus, analyses using chimeras and point mutants successfully elucidated the key residues involved in BRE VL destabilization and increased amyloidogenic propensity. These results also suggest that the modulation of surface properties of wild-type VL may improve their stability and prevent the formation of amyloid fibrils.
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Affiliation(s)
- Yuta Kobayashi
- Division of Structural Biology, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University , 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
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89
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Weltrowska G, Lemieux C, Chung NN, Guo JJ, Wilkes BC, Schiller PW. 'Carba'-carfentanil (trans isomer): a μ opioid receptor (MOR) partial agonist with a distinct binding mode. Bioorg Med Chem 2014; 22:4581-6. [PMID: 25129170 DOI: 10.1016/j.bmc.2014.07.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/15/2014] [Accepted: 07/19/2014] [Indexed: 11/16/2022]
Abstract
There is strong evidence to indicate that a positively charged nitrogen of endogenous and exogenous opioid ligands forms a salt bridge with the Asp residue in the third transmembrane helix of opioid receptors. To further examine the role of this electrostatic interaction in opioid receptor binding and activation, we synthesized 'carba'-analogues of the highly potent μ opioid analgesic carfentanil (3), in which the piperidine nitrogen was replaced with a carbon. The resulting trans isomer (8b) showed reduced, but still significant MOR binding affinity (Ki(μ)=95.2nM) with no MOR versus DOR binding selectivity and was a MOR partial agonist. The cis isomer (8a) was essentially inactive. A MOR docking study indicated that 8b bound to the same binding pocket as parent 3, but its binding mode was somewhat different. A re-evaluation of the uncharged morphine derivative N-formylnormorphine (9) indicated that it was a weak MOR antagonist showing no preference for MOR over KOR. Taken together, the results indicate that deletion of the positively charged nitrogen in μ opioid analgesics reduces MOR binding affinity by 2-3 orders of magnitude and may have pronounced effects on the intrinsic efficacy and on the opioid receptor selectivity profile.
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Affiliation(s)
- Grazyna Weltrowska
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada
| | - Carole Lemieux
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada
| | - Nga N Chung
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada
| | - Jason J Guo
- Center for Drug Discovery, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Brian C Wilkes
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada
| | - Peter W Schiller
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Department of Pharmacology, Université de Montréal, Montreal, QC H3C 3J7, Canada.
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90
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Kaur R, Ramesh M, Bharatam PV, Kishore R. Self-Association Behavior of a Novel Nonproteinogenic β-Strand-Mimic in an Organic Solvent. J Phys Chem B 2014; 118:9199-208. [DOI: 10.1021/jp5042074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajwant Kaur
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh−160 036, India
| | - Muthusamy Ramesh
- National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar−160 062, Punjab, India
| | - Prasad V. Bharatam
- National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar−160 062, Punjab, India
| | - Raghuvansh Kishore
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh−160 036, India
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91
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Pandyarajan V, Phillips NB, Cox GP, Yang Y, Whittaker J, Ismail-Beigi F, Weiss MA. Biophysical optimization of a therapeutic protein by nonstandard mutagenesis: studies of an iodo-insulin derivative. J Biol Chem 2014; 289:23367-81. [PMID: 24993826 DOI: 10.1074/jbc.m114.588277] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Insulin provides a model for the therapeutic application of protein engineering. A paradigm in molecular pharmacology was defined by design of rapid-acting insulin analogs for the prandial control of glycemia. Such analogs, a cornerstone of current diabetes regimens, exhibit accelerated subcutaneous absorption due to more rapid disassembly of oligomeric species relative to wild-type insulin. This strategy is limited by a molecular trade-off between accelerated disassembly and enhanced susceptibility to degradation. Here, we demonstrate that this trade-off may be circumvented by nonstandard mutagenesis. Our studies employed Lys(B28), Pro(B29)-insulin ("lispro") as a model prandial analog that is less thermodynamically stable and more susceptible to fibrillation than is wild-type insulin. We have discovered that substitution of an invariant tyrosine adjoining the engineered sites in lispro (Tyr(B26)) by 3-iodo-Tyr (i) augments its thermodynamic stability (ΔΔGu 0.5 ± 0.2 kcal/mol), (ii) delays onset of fibrillation (lag time on gentle agitation at 37 °C was prolonged by 4-fold), (iii) enhances affinity for the insulin receptor (1.5 ± 0.1-fold), and (iv) preserves biological activity in a rat model of diabetes mellitus. (1)H NMR studies suggest that the bulky iodo-substituent packs within a nonpolar interchain crevice. Remarkably, the 3-iodo-Tyr(B26) modification stabilizes an oligomeric form of insulin pertinent to pharmaceutical formulation (the R6 zinc hexamer) but preserves rapid disassembly of the oligomeric form pertinent to subcutaneous absorption (T6 hexamer). By exploiting this allosteric switch, 3-iodo-Tyr(B26)-lispro thus illustrates how a nonstandard amino acid substitution can mitigate the unfavorable biophysical properties of an engineered protein while retaining its advantages.
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Affiliation(s)
| | | | | | | | | | | | - Michael A Weiss
- From the Departments of Biochemistry, Medicine, and Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106
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92
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Karunarathna AAS, Saebo S. Computational studies of the intermolecular interactions in dimers of the bowl-shaped sumanene molecule. Struct Chem 2014. [DOI: 10.1007/s11224-014-0463-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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93
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Janke R, Görner C, Hirte M, Brück T, Loll B. The first structure of a bacterial diterpene cyclase: CotB2. ACTA ACUST UNITED AC 2014; 70:1528-37. [PMID: 24914964 DOI: 10.1107/s1399004714005513] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/11/2014] [Indexed: 02/05/2023]
Abstract
Sesquiterpenes and diterpenes are a diverse class of secondary metabolites that are predominantly derived from plants and some prokaryotes. The properties of these natural products encompass antitumor, antibiotic and even insecticidal activities. Therefore, they are interesting commercial targets for the chemical and pharmaceutical industries. Owing to their structural complexity, these compounds are more efficiently accessed by metabolic engineering of microbial systems than by chemical synthesis. This work presents the first crystal structure of a bacterial diterpene cyclase, CotB2 from the soil bacterium Streptomyces melanosporofaciens, at 1.64 Å resolution. CotB2 is a diterpene cyclase that catalyzes the cyclization of the linear geranylgeranyl diphosphate to the tricyclic cyclooctat-9-en-7-ol. The subsequent oxidation of cyclooctat-9-en-7-ol by two cytochrome P450 monooxygenases leads to bioactive cyclooctatin. Plasticity residues that decorate the active site of CotB2 have been mutated, resulting in alternative monocyclic, dicyclic and tricyclic compounds that show bioactivity. These new compounds shed new light on diterpene cyclase reaction mechanisms. Furthermore, the product of mutant CotB2(W288G) produced the new antibiotic compound (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene, which acts specifically against multidrug-resistant Staphylococcus aureus. This opens a sustainable route for the industrial-scale production of this bioactive compound.
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Affiliation(s)
- Ronja Janke
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Christian Görner
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Max Hirte
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Thomas Brück
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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94
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Gardarsson H, Schweizer WB, Trapp N, Diederich F. Structures and Properties of Molecular Torsion Balances to Decipher the Nature of Substituent Effects on the Aromatic Edge-to-Face Interaction. Chemistry 2014; 20:4608-16. [DOI: 10.1002/chem.201304810] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 11/10/2022]
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95
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Peselis A, Serganov A. Themes and variations in riboswitch structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:908-918. [PMID: 24583553 DOI: 10.1016/j.bbagrm.2014.02.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/14/2014] [Accepted: 02/20/2014] [Indexed: 11/19/2022]
Abstract
The complexity of gene expression control by non-coding RNA has been highlighted by the recent progress in the field of riboswitches. Discovered a decade ago, riboswitches represent a diverse group of non-coding mRNA regions that possess a unique ability to directly sense cellular metabolites and modulate gene expression through formation of alternative metabolite-free and metabolite-bound conformations. Such protein-free metabolite sensing domains utilize sophisticated three-dimensional folding of RNA molecules to discriminate between a cognate ligand from related compounds so that only the right ligand would trigger a genetic response. Given the variety of riboswitch ligands ranging from small cations to large coenzymes, riboswitches adopt a great diversity of structures. Although many riboswitches share structural principles to build metabolite-competent folds, form precise ligand-binding pockets, and communicate a ligand-binding event to downstream regulatory regions, virtually all riboswitch classes possess unique features for ligand recognition, even those tuned to recognize the same metabolites. Here we present an overview of the biochemical and structural research on riboswitches with a major focus on common principles and individual characteristics adopted by these regulatory RNA elements during evolution to specifically target small molecules and exert genetic responses. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA.
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96
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Zaidi S, Hassan MI, Islam A, Ahmad F. The role of key residues in structure, function, and stability of cytochrome-c. Cell Mol Life Sci 2014; 71:229-55. [PMID: 23615770 PMCID: PMC11113841 DOI: 10.1007/s00018-013-1341-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 02/06/2023]
Abstract
Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.
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Affiliation(s)
- Sobia Zaidi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
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97
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Theoretical studies of the interaction between influenza virus hemagglutinin and its small molecule ligands. J Mol Model 2013; 19:5561-8. [DOI: 10.1007/s00894-013-2036-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
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98
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Ahmad E, Rabbani G, Zaidi N, Khan MA, Qadeer A, Ishtikhar M, Singh S, Khan RH. Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges. J Biomol Struct Dyn 2013; 31:630-48. [DOI: 10.1080/07391102.2012.706081] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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99
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Sivasakthi V, Anitha P, Kumar KM, Bag S, Senthilvel P, Lavanya P, Swetha R, Anbarasu A, Ramaiah S. Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins. Bioinformation 2013; 9:432-9. [PMID: 23750094 PMCID: PMC3670127 DOI: 10.6026/97320630009432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 04/06/2013] [Indexed: 11/23/2022] Open
Abstract
Aromatic-aromatic hydrogen bonds are important in many areas of chemistry, biology and materials science. In this study we have analyzed the roles played by the π-π interactions in interleukins (ILs) and tumor necrosis factor (TNF) proteins. Majority of π-π interacting residues are conserved in ILs and TNF proteins. The accessible surface area calculations in these proteins reveal that these interactions might be important in stabilizing the inner core regions of these proteins. In addition to π-π interactions, the aromatic residues also form π-networks in ILs and TNF proteins. The results obtained in the present study indicate that π-π interactions and π-π networks play important roles in the structural stability of ILs and TNF proteins.
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Affiliation(s)
- Vaideeswaran Sivasakthi
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
| | - Parimelzaghan Anitha
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
| | - Kalavathi Murugan Kumar
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
| | - Susmita Bag
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
| | - Padmanaban Senthilvel
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
| | - Pandian Lavanya
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
| | - Rayapadi Swetha
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
| | - Anand Anbarasu
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
| | - Sudha Ramaiah
- Bioinformatics Division, School of Biosciences & Technology, VIT University, Vellore-632014, India
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100
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Borges A, Cordeiro JM. Hydrogen bonding donation of N-methylformamide with dimethylsulfoxide and water. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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