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da Rocha JM, Campos DMDO, Esmaile SC, Menezes GDL, Bezerra KS, da Silva RA, Junior EDDS, Tayyeb JZ, Akash S, Fulco UL, Alqahtani T, Oliveira JIN. Quantum biochemical analysis of the binding interactions between a potential inhibitory drug and the Ebola viral glycoprotein. J Biomol Struct Dyn 2024:1-17. [PMID: 38258414 DOI: 10.1080/07391102.2024.2305314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024]
Abstract
Ebola virus disease (EVD) causes outbreaks and epidemics in West Africa that persist until today. The envelope glycoprotein of Ebola virus (GP) consists of two subunits, GP1 and GP2, and plays a key role in anchoring or fusing the virus to the host cell in its active form on the virion surface. Toremifene (TOR) is a ligand that mainly acts as an estrogen receptor antagonist; however, a recent study showed a strong and efficient interaction with GP. In this context, we aimed to evaluate the energetic affinity features involved in the interaction between GP and toremifene by computer simulation techniques using the Molecular Fractionation Method with Conjugate Caps (MFCC) scheme and quantum-mechanical (QM) calculations, as well as missense mutations to assess protein stability. We identified ASP522, GLU100, TYR517, THR519, LEU186, LEU515 as the most attractive residues in the EBOV glycoprotein structure that form the binding pocket. We divided toremifene into three regions and evaluated that region i was more important than region iii and region ii for the formation of the TOR-GP1/GP2 complex, which might control the molecular remodeling process of TOR. The mutations that caused more destabilization were ARG134, LEU515, TYR517 and ARG559, while those that caused stabilization were GLU523 and ASP522. TYR517 is a critical residue for the binding of TOR, and is highly conserved among EBOV species. Our results may help to elucidate the mechanism of drug action on the GP protein of the Ebola virus and subsequently develop new pharmacological approaches against EVD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jaerdyson M da Rocha
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel M de O Campos
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Stephany C Esmaile
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Gabriela de L Menezes
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Katyanna S Bezerra
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Roosevelt A da Silva
- Core Collaboratives of BioSistemas, Special Unit of Exact Sciences, Federal University of Jataí, Jataí, GO, Brazil
| | - Edilson D da S Junior
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Jehad Zuhair Tayyeb
- Department of Clinical Biochemistry, College of Medicine, University of Jeddah, Jeddah, Saudi Arabia
| | - Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, Bangladesh
| | - Umberto L Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Jonas I N Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
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Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
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Ayipo YO, Alananzeh WA, Ahmad I, Patel H, Mordi MN. Structural modelling and in silico pharmacology of β-carboline alkaloids as potent 5-HT1A receptor antagonists and reuptake inhibitors. J Biomol Struct Dyn 2022:1-17. [PMID: 35881145 DOI: 10.1080/07391102.2022.2104376] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Serotonin (5-HT) antagonists and reuptake inhibitors (SARIs) are atypical antidepressants for managing major depressive disorder. They are oftentimes applied as adjuvants for ameliorating aftereffects of SSRI antidepressants including insomnia and sexual dysfunction. The few available candidates of this class including lorpiprazole and trazodone also display some daunting side effects, making a continuous search for improved alternatives essential. Natural β-carboline alkaloids (NβCs) are interestingly renowned with broad pharmacological spectrum against several neuropsychiatric disorders including depression. However, their potentials as SARIs remain underexplored. In this study, 982 NβCs retrieved from the Ambinter-Greenpharma (Amb) database were virtually screened for potent SARI alternatives using computational and biocheminformatics approaches: homology modelling of 5-HT1A receptor, Glide HTVS, SP and XP molecular docking, molecular dynamics (MD) simulation, ADMET and mutagenicity predictions. The homology receptor was validated as a good representative of human 5HT1A receptor using the RCSB structure validation and quality protocols. From the virtual screening against the 5-HT1A receptor, Amb ligands, Amb18709727 and Amb37857532 showed higher binding affinities by XP scores of -8.725 and -7.976 kcal/mol, and MMGBSA of -87.972 and -107.585 kcal/mol respectively compared to lorpiprazole, a reference SARI with XP score and MMGBSA of -6.512 and -62.788 kcal/mol respectively. They maintained ideal contacts with pharmacologically essential amino acid residues implicated in SARI mechanisms and expressed higher stability and compactness than lorpiprazole throughout the trajectories of 100 ns MD simulation. They also displayed interesting ADME, druggability, low toxicity and mutagenicity profiles, ideal for CNS drug prospects, thus, recommended as putative SARI candidates for further study.
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Affiliation(s)
- Yusuf Oloruntoyin Ayipo
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia.,Department of Chemistry and Industrial Chemistry, Kwara State University, Malete, Ilorin, Nigeria
| | - Waleed A Alananzeh
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Mohd Nizam Mordi
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
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4
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Eichinger A, Rauth S, Hinz D, Feuerbach A, Skerra A. Structural basis of Alzheimer β-amyloid peptide recognition by engineered lipocalin proteins with aggregation-blocking activity. Biol Chem 2022; 403:557-571. [PMID: 35355502 DOI: 10.1515/hsz-2021-0375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/09/2022] [Indexed: 11/15/2022]
Abstract
We describe the structural analysis of two Anticalin® proteins that tightly bind Aβ 40, a peptide involved in the pathophysiology of Alzheimer's disease. These anticalins, US7 and H1GA, were engineered on the basis of the human lipocalin 2, thus yielding compact single-domain binding proteins as an alternative to antibodies. Albeit selected under different conditions and mutually deviating in 13 amino acid positions within the binding pocket (of 17 mutated residues in total), both crystallised anticalins recognize the same epitope in the middle of the β-amyloid peptide. In the two complexes with the Aβ 40 peptide, its central part comprising residues LysP16 to LysP28 shows well defined electron density whereas the flanking regions appear structurally disordered. The compact zigzag-bend conformation which is seen in both structures may indicate a role during conversion of the soluble monomeric form into pathogenic Aβ state(s) and, thus, explain the aggregation-inhibiting effect of the anticalins. In contrast to solanezumab, which targets the same Aβ region in a different conformation, the anticalin H1GA does not show cross-reactivity with sequence-related human plasma proteins. Consequently, anticalins offer promising reagents to prevent oligomerization of Aβ peptides to neurotoxic species in vivo and their small size may enable new routes for brain delivery.
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Affiliation(s)
- Andreas Eichinger
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, D-85354 Freising, Germany
| | - Sabine Rauth
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, D-85354 Freising, Germany
| | - Dominik Hinz
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, D-85354 Freising, Germany
| | - Anna Feuerbach
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, D-85354 Freising, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, D-85354 Freising, Germany
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Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK. A practical guide to large-scale docking. Nat Protoc 2021; 16:4799-4832. [PMID: 34561691 PMCID: PMC8522653 DOI: 10.1038/s41596-021-00597-z] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/22/2021] [Indexed: 02/08/2023]
Abstract
Structure-based docking screens of large compound libraries have become common in early drug and probe discovery. As computer efficiency has improved and compound libraries have grown, the ability to screen hundreds of millions, and even billions, of compounds has become feasible for modest-sized computer clusters. This allows the rapid and cost-effective exploration and categorization of vast chemical space into a subset enriched with potential hits for a given target. To accomplish this goal at speed, approximations are used that result in undersampling of possible configurations and inaccurate predictions of absolute binding energies. Accordingly, it is important to establish controls, as are common in other fields, to enhance the likelihood of success in spite of these challenges. Here we outline best practices and control docking calculations that help evaluate docking parameters for a given target prior to undertaking a large-scale prospective screen, with exemplification in one particular target, the melatonin receptor, where following this procedure led to direct docking hits with activities in the subnanomolar range. Additional controls are suggested to ensure specific activity for experimentally validated hit compounds. These guidelines should be useful regardless of the docking software used. Docking software described in the outlined protocol (DOCK3.7) is made freely available for academic research to explore new hits for a range of targets.
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Affiliation(s)
- Brian J Bender
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - Andreas Luttens
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jiankun Lyu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - Chase M Webb
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - Reed M Stein
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - Elissa A Fink
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - Trent E Balius
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
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Eichinger A, Neumaier I, Skerra A. The extracellular region of bovine milk butyrophilin exhibits closer structural similarity to human myelin oligodendrocyte glycoprotein than to immunological BTN family receptors. Biol Chem 2021; 402:1187-1202. [PMID: 34342946 DOI: 10.1515/hsz-2021-0122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/17/2021] [Indexed: 11/15/2022]
Abstract
Bovine butyrophilin (BTN1A1) is an abundant type I transmembrane glycoprotein exposed on the surface of milk fat globules. We have solved the crystal structure of its extracellular region via multiple wavelength anomalous dispersion after incorporation of selenomethionine into the bacterially produced protein. The butyrophilin ectodomain exhibits two subdomains with immunoglobulin fold, each comprising a β-sandwich with a central disulfide bridge as well as one N-linked glycosylation. The fifth Cys residue at position 193 is unpaired and prone to forming disulfide crosslinks. The apparent lack of a ligand-binding site or receptor activity suggests a function predominantly as hydrophilic coat protein to prevent coagulation of the milk fat droplets. While there is less structural resemblance to members of the human butyrophilin family such as BTN3A, which play a role as immune receptors, the N-terminal bovine butyrophilin subdomain shows surprising similarity to the human myelin oligodendrocyte glycoprotein, a protein exposed on the surface of myelin sheaths. Thus, our study lends structural support to earlier hypotheses of a correlation between the consumption of cow milk and prevalence of neurological autoimmune diseases and may offer guidance for the breeding of cattle strains that express modified butyrophilin showing less immunological cross-reactivity.
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Affiliation(s)
- Andreas Eichinger
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, D-85354 Freising, Germany
| | - Irmgard Neumaier
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, D-85354 Freising, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, D-85354 Freising, Germany
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7
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Peplau E, De Rose F, Eichinger A, Reder S, Mittelhäuser M, Scafetta G, Schwaiger M, Weber WA, Bartolazzi A, D'Alessandria C, Skerra A. Effective rational humanization of a PASylated anti-galectin-3 Fab for the sensitive PET imaging of thyroid cancer in vivo. Sci Rep 2021; 11:7358. [PMID: 33795750 PMCID: PMC8016950 DOI: 10.1038/s41598-021-86641-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The lack of a non-invasive test for malignant thyroid nodules makes the diagnosis of thyroid cancer (TC) challenging. Human galectin-3 (hGal3) has emerged as a promising target for medical TC imaging and diagnosis because of its exclusive overexpression in malignant thyroid tissues. We previously developed a human-chimeric αhGal3 Fab fragment derived from the rat monoclonal antibody (mAb) M3/38 with optimized clearance characteristics using PASylation technology. Here, we describe the elucidation of the hGal3 epitope recognized by mAb M3/38, X-ray crystallographic analysis of its complex with the chimeric Fab and, based on the three-dimensional structure, the rational humanization of the Fab by CDR grafting. Four CDR-grafted versions were designed using structurally most closely related fully human immunoglobulin VH/VL regions of which one-employing the acceptor framework regions of the HIV-1 neutralizing human antibody m66-showed the highest antigen affinity. By introducing two additional back-mutations to the rodent donor sequence, an affinity toward hGal3 indistinguishable from the chimeric Fab was achieved (KD = 0.34 ± 0.02 nM in SPR). The PASylated humanized Fab was site-specifically labelled with the fluorescent dye Cy7 and applied for the immuno-histochemical staining of human tissue sections representative for different TCs. The same protein was conjugated with the metal chelator Dfo, followed by radiolabelling with 89Zr(IV). The resulting protein tracer allowed the highly sensitive and specific PET/CT imaging of orthotopic tumors in mice, which was confirmed by quantitative analysis of radiotracer accumulation. Thus, the PASylated humanized αhGal3 Fab offers clinical potential for the diagnostic imaging of TC.
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Affiliation(s)
- Emanuel Peplau
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany
| | - Francesco De Rose
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Andreas Eichinger
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany
| | - Sybille Reder
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Markus Mittelhäuser
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Giorgia Scafetta
- Pathology Research Laboratory, Sant'Andrea Hospital, University Sapienza, via di Grottarossa 1035, 00189, Rome, Italy
| | - Markus Schwaiger
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Wolfgang A Weber
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Armando Bartolazzi
- Pathology Research Laboratory, Cancer Center Karolinska, Karolinska Hospital, 17176, Stockholm, Sweden
- Pathology Research Laboratory, Sant'Andrea Hospital, University Sapienza, via di Grottarossa 1035, 00189, Rome, Italy
| | - Calogero D'Alessandria
- Klinikum rechts der Isar, Nuclear Medicine Department, Technical University Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany.
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Cholesterol content in the membrane promotes key lipid-protein interactions in a pentameric serotonin-gated ion channel. Biointerphases 2021; 15:061018. [PMID: 33397116 DOI: 10.1116/6.0000561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs), embedded in the lipid membranes of nerve cells, mediate fast synaptic transmission and are major pharmaceutical targets. Because of their complexity and the limited knowledge of their structure, their working mechanisms have still to be fully unraveled at the molecular level. Over the past few years, evidence that the lipid membrane may modulate the function of membrane proteins, including pLGICs, has emerged. Here, we investigate, by means of molecular dynamics simulations, the behavior of the lipid membrane at the interface with the 5-HT3A receptor (5-HT3AR), a representative pLGIC which is the target of nausea-suppressant drugs, in a nonconductive state. Three lipid compositions are studied, spanning different concentrations of the phospholipids, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, and of cholesterol, hence a range of viscosities. A variety of lipid interactions and persistent binding events to different parts of the receptor are revealed in the investigated models, providing snapshots of the dynamical environment at the membrane-receptor interface. Some of these events result in lipid intercalation within the transmembrane domain, and others reach out to protein key sections for signal transmission and receptor activation, such as the Cys-loop and the M2-M3 loop. In particular, phospholipids, with their long hydrophobic tails, play an important role in these interactions, potentially providing a bridge between these two structures. A higher cholesterol content appears to promote lipid persistent binding to the receptor.
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Esmaile SC, Bezerra KS, de Oliveira Campos DM, da Silva MK, Neto JXL, Manzoni V, Fulco UL, Oliveira JIN. Quantum binding energy features of the drug olmesartan bound to angiotensin type-1 receptors in the therapeutics of stroke. NEW J CHEM 2021. [DOI: 10.1039/d1nj03975j] [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]
Abstract
We investigated the binding energies of 105 residues within a 10 Å pocket radius, predicted the energetic relevance of olmesartan regions, and the influence of individual protein segments on OLM -AT1 binding.
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Affiliation(s)
- Stephany Campanelli Esmaile
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - Katyanna Sales Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | | | - Maria Karolaynne da Silva
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - José Xavier Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - Vinicius Manzoni
- Instituto de Física, Universidade Federal de Alagoas, 57072-970, Maceio, AL, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - Jonas Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
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An engineered lipocalin that tightly complexes the plant poison colchicine for use as antidote and in bioanalytical applications. Biol Chem 2018; 400:351-366. [DOI: 10.1515/hsz-2018-0342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023]
Abstract
Abstract
Colchicine is a toxic alkaloid prevalent in autumn crocus (Colchicum autumnale) that binds to tubulin and inhibits polymerization of microtubules. Using combinatorial and rational protein design, we have developed an artificial binding protein based on the human lipocalin 2 that binds colchicine with a dissociation constant of 120 pm, i.e. 10000-fold stronger than tubulin. Crystallographic analysis of the engineered lipocalin, dubbed Colchicalin, revealed major structural changes in the flexible loop region that forms the ligand pocket at the open end of the eight-stranded β-barrel, resulting in a lid-like structure over the deeply buried colchicine. A cis-peptide bond between residues Phe71 and Pro72 in loop #2 constitutes a peculiar feature and allows intimate contact with the tricyclic ligand. Using directed evolution, we achieved an extraordinary dissociation half-life of more than 9 h for the Colchicalin-colchicine complex. Together with the chemical robustness of colchicine and availability of activated derivatives, this also opens applications as a general-purpose affinity reagent, including facile quantification of colchicine in biological samples. Given that engineered lipocalins, also known as Anticalin® proteins, represent a class of clinically validated biopharmaceuticals, Colchicalin may offer a therapeutic antidote to scavenge colchicine and reverse its poisoning effect in situations of acute intoxication.
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11
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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12
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Hoffmann T, Marion A, Antes I. DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles. BMC STRUCTURAL BIOLOGY 2017; 17:2. [PMID: 28148269 PMCID: PMC5289058 DOI: 10.1186/s12900-016-0071-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 12/29/2016] [Indexed: 11/22/2022]
Abstract
Background T cell receptor (TCR) molecules are involved in the adaptive immune response as they distinguish between self- and foreign-peptides, presented in major histocompatibility complex molecules (pMHC). Former studies showed that the association angles of the TCR variable domains (Vα/Vβ) can differ significantly and change upon binding to the pMHC complex. These changes can be described as a rotation of the domains around a general Center of Rotation, characterized by the interaction of two highly conserved glutamine residues. Methods We developed a computational method, DynaDom, for the prediction of TCR Vα/Vβ inter-domain and TCR/pMHC orientations in TCRpMHC complexes, which allows predicting the orientation of multiple protein-domains. In addition, we implemented a new approach to predict the correct orientation of the carboxamide endgroups in glutamine and asparagine residues, which can also be used as an external, independent tool. Results The approach was evaluated for the remodeling of 75 and 53 experimental structures of TCR and TCRpMHC (class I) complexes, respectively. We show that the DynaDom method predicts the correct orientation of the TCR Vα/Vβ angles in 96 and 89% of the cases, for the poses with the best RMSD and best interaction energy, respectively. For the concurrent prediction of the TCR Vα/Vβ and pMHC orientations, the respective rates reached 74 and 72%. Through an exhaustive analysis, we could show that the pMHC placement can be further improved by a straightforward, yet very time intensive extension of the current approach. Conclusions The results obtained in the present remodeling study prove the suitability of our approach for interdomain-angle optimization. In addition, the high prediction rate obtained specifically for the energetically highest ranked poses further demonstrates that our method is a powerful candidate for blind prediction. Therefore it should be well suited as part of any accurate atomistic modeling pipeline for TCRpMHC complexes and potentially other large molecular assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12900-016-0071-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Hoffmann
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Antoine Marion
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Iris Antes
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany.
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13
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Sinitsyn DO, Armeev GA. On the possibility of determining the structure of proteins in experiments using X-ray free electron lasers in the nonstationary scattering mode. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2017. [DOI: 10.1134/s1990793117010110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Cong X, Cremer C, Nachreiner T, Barth S, Carloni P. Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations. Protein Sci 2016; 25:1451-60. [PMID: 27110669 PMCID: PMC4972201 DOI: 10.1002/pro.2941] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/20/2016] [Indexed: 01/29/2023]
Abstract
Targeted human cytolytic fusion proteins (hCFPs) represent a new generation of immunotoxins (ITs) for the specific targeting and elimination of malignant cell populations. Unlike conventional ITs, hCFPs comprise a human/humanized target cell-specific binding moiety (e.g., an antibody or a fragment thereof) fused to a human proapoptotic protein as the cytotoxic domain (effector domain). Therefore, hCFPs are humanized ITs expected to have low immunogenicity. This reduces side effects and allows long-term application. The human ribonuclease angiogenin (Ang) has been shown to be a promising effector domain candidate. However, the application of Ang-based hCFPs is largely hampered by the intracellular placental ribonuclease inhibitor (RNH1). It rapidly binds and inactivates Ang. Mutations altering Ang's affinity for RNH1 modulate the cytotoxicity of Ang-based hCFPs. Here we perform in total 2.7 µs replica-exchange molecular dynamics simulations to investigate some of these mutations-G85R/G86R (GGRRmut ), Q117G (QGmut ), and G85R/G86R/Q117G (GGRR/QGmut ). GGRRmut turns out to perturb greatly the overall Ang-RNH1 interactions, whereas QGmut optimizes them. Combining QGmut with GGRRmut compensates the effects of the latter. Our results explain the in vitro finding that, while Ang GGRRmut -based hCFPs resist RNH1 inhibition remarkably, Ang WT- and Ang QGmut -based ones are similarly sensitive to RNH1 inhibition, whereas Ang GGRR/QGmut -based ones are only slightly resistant. This work may help design novel Ang mutants with reduced affinity for RNH1 and improved cytotoxicity.
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Affiliation(s)
- Xiaojing Cong
- Computational Biophysics, German Research School for Simulation Sciences (Joint Venture of RWTH Aachen University and Forschungszentrum Jülich)Jülich52428Germany
- Computational Biomedicine Section, Institute for Advanced Simulations ‐ 5 (IAS‐5)Jülich52428GermanyForschungszentrum Jülich
- Computational Biomedicine Section, Institute for Neuroscience and Medicine ‐ 9 (INM‐9)Jülich52428GermanyForschungszentrum Jülich
| | - Christian Cremer
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical EngineeringUniversity Hospital RWTH AachenAachen52074Germany
| | - Thomas Nachreiner
- Department of Experimental Medicine and Immunotherapy, Institute for Applied Medical EngineeringUniversity Hospital RWTH AachenAachen52074Germany
| | - Stefan Barth
- Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape TownCape Town7925South Africa
- South African Research Chair in Cancer Biotechnology, Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape Town7925Cape TownSouth Africa
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences (Joint Venture of RWTH Aachen University and Forschungszentrum Jülich)Jülich52428Germany
- Computational Biomedicine Section, Institute for Advanced Simulations ‐ 5 (IAS‐5)Jülich52428GermanyForschungszentrum Jülich
- Computational Biomedicine Section, Institute for Neuroscience and Medicine ‐ 9 (INM‐9)Jülich52428GermanyForschungszentrum Jülich
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15
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Deller MC, Rupp B. Models of protein-ligand crystal structures: trust, but verify. J Comput Aided Mol Des 2015; 29:817-36. [PMID: 25665575 PMCID: PMC4531100 DOI: 10.1007/s10822-015-9833-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/29/2015] [Indexed: 11/26/2022]
Abstract
X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.
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Affiliation(s)
- Marc C Deller
- The Joint Center for Structural Genomics, San Diego, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bernhard Rupp
- , k.-k. Hofkristallamt 991 Audrey Place, Vista, CA, 92084, USA.
- Department of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstr. 41, 6020, Innsbruck, Austria.
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16
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Cong X, Campomanes P, Kless A, Schapitz I, Wagener M, Koch T, Carloni P. Structural Determinants for the Binding of Morphinan Agonists to the μ-Opioid Receptor. PLoS One 2015; 10:e0135998. [PMID: 26280453 PMCID: PMC4539194 DOI: 10.1371/journal.pone.0135998] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/28/2015] [Indexed: 01/05/2023] Open
Abstract
Atomistic descriptions of the μ-opioid receptor (μOR) noncovalently binding with two of its prototypical morphinan agonists, morphine (MOP) and hydromorphone (HMP), are investigated using molecular dynamics (MD) simulations. Subtle differences between the binding modes and hydration properties of MOP and HMP emerge from the calculations. Alchemical free energy perturbation calculations show qualitative agreement with in vitro experiments performed in this work: indeed, the binding free energy difference between MOP and HMP computed by forward and backward alchemical transformation is 1.2±1.1 and 0.8±0.8 kcal/mol, respectively, to be compared with 0.4±0.3 kcal/mol from experiment. Comparison with an MD simulation of μOR covalently bound with the antagonist β-funaltrexamine hints to agonist-induced conformational changes associated with an early event of the receptor’s activation: a shift of the transmembrane helix 6 relative to the transmembrane helix 3 and a consequent loss of the key R165-T279 interhelical hydrogen bond. This finding is consistent with a previous proposal suggesting that the R165-T279 hydrogen bond between these two helices indicates an inactive receptor conformation.
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Affiliation(s)
- Xiaojing Cong
- Laboratory of Computational Biophysics, German Research School for Simulation Sciences GmbH, Joint venture of RWTH Aachen University and Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine section (IAS-5), Institute of Advanced Simulation (IAS), Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine section (INM-9), Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Pablo Campomanes
- Laboratory of Computational Biophysics, German Research School for Simulation Sciences GmbH, Joint venture of RWTH Aachen University and Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine section (IAS-5), Institute of Advanced Simulation (IAS), Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine section (INM-9), Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Achim Kless
- Grünenthal Innovation, Grünenthal GmbH, 52078 Aachen, Germany
| | - Inga Schapitz
- Grünenthal Innovation, Grünenthal GmbH, 52078 Aachen, Germany
| | - Markus Wagener
- Grünenthal Innovation, Grünenthal GmbH, 52078 Aachen, Germany
| | - Thomas Koch
- Grünenthal Innovation, Grünenthal GmbH, 52078 Aachen, Germany
| | - Paolo Carloni
- Laboratory of Computational Biophysics, German Research School for Simulation Sciences GmbH, Joint venture of RWTH Aachen University and Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine section (IAS-5), Institute of Advanced Simulation (IAS), Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine section (INM-9), Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, 52425 Jülich, Germany
- * E-mail:
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17
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Krepl M, Havrila M, Stadlbauer P, Banas P, Otyepka M, Pasulka J, Stefl R, Sponer J. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? J Chem Theory Comput 2015; 11:1220-43. [PMID: 26579770 DOI: 10.1021/ct5008108] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report over 30 μs of unrestrained molecular dynamics simulations of six protein-RNA complexes in explicit solvent. We utilize the AMBER ff99bsc0χ(OL3) RNA force field combined with the ff99SB protein force field and its more recent ff12SB version with reparametrized side-chain dihedrals. The simulations show variable behavior, ranging from systems that are essentially stable to systems with progressive deviations from the experimental structure, which we could not stabilize anywhere close to the starting experimental structure. For some systems, microsecond-scale simulations are necessary to achieve stabilization after initial sizable structural perturbations. The results show that simulations of protein-RNA complexes are challenging and every system should be treated individually. The simulations are affected by numerous factors, including properties of the starting structures (the initially high force field potential energy, resolution limits, conformational averaging, crystal packing, etc.), force field imbalances, and real flexibility of the studied systems. These factors, and thus the simulation behavior, differ from system to system. The structural stability of simulated systems does not correlate with the size of buried interaction surface or experimentally determined binding affinities but reflects the type of protein-RNA recognition. Protein-RNA interfaces involving shape-specific recognition of RNA are more stable than those relying on sequence-specific RNA recognition. The differences between the protein force fields are considerably smaller than the uncertainties caused by sampling and starting structures. The ff12SB improves description of the tyrosine side-chain group, which eliminates some problems associated with tyrosine dynamics.
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Affiliation(s)
- M Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - M Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - P Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - P Banas
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , Tř. 17 Listopadu 12, 771 46 Olomouc, Czech Republic
| | - M Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , Tř. 17 Listopadu 12, 771 46 Olomouc, Czech Republic
| | | | | | - J Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
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18
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Estarellas C, Otyepka M, Koča J, Banáš P, Krepl M, Šponer J. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochim Biophys Acta Gen Subj 2014; 1850:1072-1090. [PMID: 25450173 DOI: 10.1016/j.bbagen.2014.10.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/15/2014] [Accepted: 10/20/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Many prokaryotic genomes comprise Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) offering defense against foreign nucleic acids. These immune systems are conditioned by the production of small CRISPR-derived RNAs matured from long RNA precursors. This often requires a Csy4 endoribonuclease cleaving the RNA 3'-end. METHODS We report extended explicit solvent molecular dynamic (MD) simulations of Csy4/RNA complex in precursor and product states, based on X-ray structures of product and inactivated precursor (55 simulations; ~3.7μs in total). RESULTS The simulations identify double-protonated His29 and deprotonated terminal phosphate as the likely dominant protonation states consistent with the product structure. We revealed potential substates consistent with Ser148 and His29 acting as the general base and acid, respectively. The Ser148 could be straightforwardly deprotonated through solvent and could without further structural rearrangements deprotonate the nucleophile, contrasting similar studies investigating the general base role of nucleobases in ribozymes. We could not locate geometries consistent with His29 acting as general base. However, we caution that the X-ray structures do not always capture the catalytically active geometries and then the reactive structures may be unreachable by the simulation technique. CONCLUSIONS We identified potential catalytic arrangement of the Csy4/RNA complex but we also report limitations of the simulation technique. Even for the dominant protonation state we could not achieve full agreement between the simulations and the structural data. GENERAL SIGNIFICANCE Potential catalytic arrangement of the Csy4/RNA complex is found. Further, we provide unique insights into limitations of simulations of protein/RNA complexes, namely, the influence of the starting experimental structures and force field limitations. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Carolina Estarellas
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.
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19
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Skala W, Utzschneider DT, Magdolen V, Debela M, Guo S, Craik CS, Brandstetter H, Goettig P. Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity. J Biol Chem 2014; 289:34267-83. [PMID: 25326387 PMCID: PMC4256358 DOI: 10.1074/jbc.m114.598201] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Human kallikrein-related peptidase 2 (KLK2) is a tryptic serine protease predominantly expressed in prostatic tissue and secreted into prostatic fluid, a major component of seminal fluid. Most likely it activates and complements chymotryptic KLK3 (prostate-specific antigen) in cleaving seminal clotting proteins, resulting in sperm liquefaction. KLK2 belongs to the “classical” KLKs 1–3, which share an extended 99- or kallikrein loop near their non-primed substrate binding site. Here, we report the 1.9 Å crystal structures of two KLK2-small molecule inhibitor complexes. In both structures discontinuous electron density for the 99-loop indicates that this loop is largely disordered. We provide evidence that the 99-loop is responsible for two biochemical peculiarities of KLK2, i.e. reversible inhibition by micromolar Zn2+ concentrations and permanent inactivation by autocatalytic cleavage. Indeed, several 99-loop mutants of KLK2 displayed an altered susceptibility to Zn2+, which located the Zn2+ binding site at the 99-loop/active site interface. In addition, we identified an autolysis site between residues 95e and 95f in the 99-loop, whose elimination prevented the mature enzyme from limited autolysis and irreversible inactivation. An exhaustive comparison of KLK2 with related structures revealed that in the KLK family the 99-, 148-, and 220-loop exist in open and closed conformations, allowing or preventing substrate access, which extends the concept of conformational selection in trypsin-related proteases. Taken together, our novel biochemical and structural data on KLK2 identify its 99-loop as a key player in activity regulation.
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Affiliation(s)
- Wolfgang Skala
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Daniel T Utzschneider
- Klinische Forschergruppe der Frauenklinik, Klinikum rechts der Isar der TU München, D-81675 Munich, Germany
| | - Viktor Magdolen
- Klinische Forschergruppe der Frauenklinik, Klinikum rechts der Isar der TU München, D-81675 Munich, Germany
| | - Mekdes Debela
- Max-Planck-Institut for Biochemistry, Proteinase Research Group, D-82152 Martinsried, Germany, and
| | - Shihui Guo
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Hans Brandstetter
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Peter Goettig
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria,
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20
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Collette F, Renger T, Schmidt am Busch M. Revealing the functional states in the active site of BLUF photoreceptors from electrochromic shift calculations. J Phys Chem B 2014; 118:11109-19. [PMID: 25153778 PMCID: PMC4174740 DOI: 10.1021/jp506400y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/22/2014] [Indexed: 11/28/2022]
Abstract
Photoexcitation with blue light of the flavin chromophore in BLUF photoreceptors induces a switch into a metastable signaling state that is characterized by a red-shifted absorption maximum. The red shift is due to a rearrangement in the hydrogen bond pattern around Gln63 located in the immediate proximity of the isoalloxazine ring system of the chromophore. There is a long-lasting controversy between two structural models, named Q63A and Q63J in the literature, on the local conformation of the residues Gln63 and Tyr21 in the dark state of the photoreceptor. As regards the mechanistic details of the light-activation mechanism, rotation of Gln63 is opposed by tautomerism in the Q63A and Q63J models, respectively. We provide a structure-based simulation of electrochromic shifts of the flavin chromophore in the wild type and in various site-directed mutants. The excellent overall agreement between experimental and computed data allows us to evaluate the two structural models. Compelling evidence is obtained that the Q63A model is incorrect, whereas the Q63J is fully consistent with the present computations. Finally, we confirm independently that a keto-enol tautomerization of the glutamine at position 63, which was proposed as molecular mechanism for the transition between the dark and the light-adapted state, explains the measured 10 to 15 nm red shift in flavin absorption between these two states of the protein. We believe that the accurateness of our results provides evidence that the BLUF photoreceptors absorption is fine-tuned through electrostatic interactions between the chromophore and the protein matrix, and finally that the simplicity of our theoretical model is advantageous as regards easy reproducibility and further extensions.
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Affiliation(s)
- Florimond Collette
- Institut für Theoretische
Physik, Johannes Kepler Universität
Linz, Altenberger Strasse
69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische
Physik, Johannes Kepler Universität
Linz, Altenberger Strasse
69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische
Physik, Johannes Kepler Universität
Linz, Altenberger Strasse
69, 4040 Linz, Austria
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21
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Ackaert C, Kofler S, Horejs-Hoeck J, Zulehner N, Asam C, von Grafenstein S, Fuchs JE, Briza P, Liedl KR, Bohle B, Ferreira F, Brandstetter H, Oostingh GJ, Duschl A. The impact of nitration on the structure and immunogenicity of the major birch pollen allergen Bet v 1.0101. PLoS One 2014; 9:e104520. [PMID: 25126882 PMCID: PMC4134196 DOI: 10.1371/journal.pone.0104520] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/10/2014] [Indexed: 11/18/2022] Open
Abstract
Allergy prevalence has increased in industrialized countries. One contributing factor could be pollution, which can cause nitration of allergens exogenously (in the air) or endogenously (in inflamed lung tissue). We investigated the impact of nitration on both the structural and immunological behavior of the major birch pollen allergen Bet v 1.0101 to determine whether nitration might be a factor in the increased incidence of allergy. Bet v 1.0101 was nitrated with tetranitromethane. Immune effects were assessed by measuring the proliferation of specific T-cell lines (TCLs) upon stimulation with different concentrations of nitrated and unmodified allergen, and by measurement of cytokine release of monocyte-derived dendritic cells (moDCs) and primary DCs (primDCs) stimulated with nitrated versus unmodified allergen. HPLC-MS, crystallography, gel electrophoresis, amino acid analysis, size exclusion chromatography and molecular dynamics simulation were performed to characterize structural changes after nitration of the allergen. The proliferation of specific TCLs was higher upon stimulation with the nitrated allergen in comparison to the unmodified allergen. An important structural consequence of nitration was oligomerization. Moreover, analysis of the crystal structure of nitrated Bet v 1.0101 showed that amino acid residue Y83, located in the hydrophobic cavity, was nitrated to 100%. Both moDCs and primDCs showed decreased production of TH1-priming cytokines, thus favoring a TH2 response. These results implicate that nitration of Bet v 1.0101 might be a contributing factor to the observed increase in birch pollen allergy, and emphasize the importance of protein modifications in understanding the molecular basis of allergenicity.
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Affiliation(s)
- Chloé Ackaert
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Stefan Kofler
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Jutta Horejs-Hoeck
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Nora Zulehner
- Department of Pathophysiology and Allergy Research and the Christian Doppler Laboratory for Immunomodulation, Medical University of Vienna, Vienna, Austria
| | - Claudia Asam
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry/Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry/Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Peter Briza
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry/Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Barbara Bohle
- Department of Pathophysiology and Allergy Research and the Christian Doppler Laboratory for Immunomodulation, Medical University of Vienna, Vienna, Austria
| | - Fátima Ferreira
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Hans Brandstetter
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Gertie J. Oostingh
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Albert Duschl
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
- * E-mail:
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22
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Grant OC, Woods RJ. Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins. Curr Opin Struct Biol 2014; 28:47-55. [PMID: 25108191 DOI: 10.1016/j.sbi.2014.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 01/11/2023]
Abstract
Impressive improvements in docking performance can be achieved by applying energy bonuses to poses in which glycan hydroxyl groups occupy positions otherwise preferred by bound waters. In addition, inclusion of glycosidic conformational energies allows unlikely glycan conformations to be appropriately penalized. A method for predicting the binding specificity of glycan-binding proteins has been developed, which is based on grafting glycan branches onto a minimal binding determinant in the binding site. Grafting can be used either to screen virtual libraries of glycans, such as the known glycome, or to identify docked poses of minimal binding determinants that are consistent with specificity data. The reviewed advances allow accurate modelling of carbohydrate-protein 3D co-complexes, but challenges remain in ranking the affinity of congeners.
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Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States; School of Chemistry, University Road, National University of Ireland, Galway, Ireland.
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23
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Structure-guided engineering of Anticalins with improved binding behavior and biochemical characteristics for application in radio-immuno imaging and/or therapy. J Struct Biol 2014; 185:203-14. [DOI: 10.1016/j.jsb.2013.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/04/2013] [Accepted: 03/18/2013] [Indexed: 11/21/2022]
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24
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Kofler S, Ackaert C, Samonig M, Asam C, Briza P, Horejs-Hoeck J, Cabrele C, Ferreira F, Duschl A, Huber C, Brandstetter H. Stabilization of the dimeric birch pollen allergen Bet v 1 impacts its immunological properties. J Biol Chem 2013; 289:540-51. [PMID: 24253036 PMCID: PMC3879576 DOI: 10.1074/jbc.m113.518795] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Many allergens share several biophysical characteristics, including the capability to undergo oligomerization. The dimerization mechanism in Bet v 1 and its allergenic properties are so far poorly understood. Here, we report crystal structures of dimeric Bet v 1, revealing a noncanonical incorporation of cysteine at position 5 instead of genetically encoded tyrosine. Cysteine polysulfide bridging stabilized different dimeric assemblies, depending on the polysulfide linker length. These dimers represent quaternary arrangements that are frequently observed in related proteins, reflecting their prevalence in unmodified Bet v 1. These conclusions were corroborated by characteristic immunologic properties of monomeric and dimeric allergen variants. Hereby, residue 5 could be identified as an allergenic hot spot in Bet v 1. The presented results refine fundamental principles in protein chemistry and emphasize the importance of protein modifications in understanding the molecular basis of allergenicity.
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Affiliation(s)
- Stefan Kofler
- From the Structural Biology Group, Department of Molecular Biology
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25
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Eckhard U, Schönauer E, Brandstetter H. Structural basis for activity regulation and substrate preference of clostridial collagenases G, H, and T. J Biol Chem 2013; 288:20184-94. [PMID: 23703618 PMCID: PMC3711286 DOI: 10.1074/jbc.m112.448548] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Clostridial collagenases are among the most efficient enzymes to degrade by far the most predominant protein in the biosphere. Here we present crystal structures of the peptidases of three clostridial collagenase isoforms (ColG, ColH, and ColT). The comparison of unliganded and liganded structures reveals a quaternary subdomain dynamics. In the unliganded ColH structure, this globular dynamics is modulated by an aspartate switch motion that binds to the catalytic zinc. We further identified a calcium binding site in proximity to the catalytic zinc. Both ions are required for full activity, explaining why calcium critically affects the enzymatic activity of clostridial collagenases. Our studies further reveal that loops close to the active site thus serve as characteristic substrate selectivity filter. These elements explain the distinct peptidolytic and collagenolytic activities of these enzymes and provide a rational framework to engineer collagenases with customized substrate specificity as well as for inhibitor design.
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Affiliation(s)
- Ulrich Eckhard
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
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26
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Zögg T, Sponring M, Schindler S, Koll M, Schneider R, Brandstetter H, Auer B. Crystal structures of the viral protease Npro imply distinct roles for the catalytic water in catalysis. Structure 2013; 21:929-38. [PMID: 23643950 PMCID: PMC3677099 DOI: 10.1016/j.str.2013.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/22/2013] [Accepted: 04/01/2013] [Indexed: 11/30/2022]
Abstract
Npro is a key effector protein of pestiviruses such as bovine viral diarrhea virus and abolishes host cell antiviral defense mechanisms. Synthesized as the N-terminal part of the viral polyprotein, Npro releases itself via an autoproteolytic cleavage, triggering its immunological functions. However, the mechanisms of its proteolytic action and its immune escape were unclear. Here, we present the crystal structures of Npro to 1.25 Å resolution. Structures of pre- and postcleavage intermediates identify three catalytically relevant elements. The trapping of the putative catalytic water reveals its distinct roles as a base, acid, and nucleophile. The presentation of the substrate further explains the enigmatic latency of the protease, ensuring a single in cis cleavage. Additionally, we identified a zinc-free, disulfide-linked conformation of the TRASH motif, an interaction hub of immune factors. The structure opens additional opportunities in utilizing Npro as an autocleaving fusion protein and as a pharmaceutical target. Putative catalytic water reveals distinct roles as a base, acid, and nucleophile The structural mechanism explains a single in cis cleavage The bimodular architecture reflects proteolytic and immunological functions The structure provides two orthogonal targets for therapy
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Affiliation(s)
- Thomas Zögg
- Department of Molecular Biology, University of Salzburg, Billrothstraße 11, 5020 Salzburg, Austria
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27
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Olivella M, Caltabiano G, Cordomí A. The role of Cysteine 6.47 in class A GPCRs. BMC STRUCTURAL BIOLOGY 2013; 13:3. [PMID: 23497259 PMCID: PMC3610275 DOI: 10.1186/1472-6807-13-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/06/2013] [Indexed: 11/10/2022]
Abstract
Background The CWxP motif of transmembrane helix 6 (x: any residue) is highly conserved in class A GPCRs. Within this motif, W6.48 is a big star in the theory of the global “toggle switch” because of its key role in the activation mechanism of GPCRs upon ligand binding. With all footlights focused on W6.48, the reason why the preceding residue, C6.47, is largely conserved is still unknown. The present study is aimed to fill up this lack of knowledge by characterizing the role of C6.47 of the CWxP motif. Results A complete analysis of available crystal structures has been made alongside with molecular dynamics simulations of model peptides to explore a possible structural role for C6.47. Conclusions We conclude that C6.47 does not modulate the conformation of the TM6 proline kink and propose that C6.47 participates in the rearrangement of the TM6 and TM7 interface accompanying activation.
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Affiliation(s)
- Mireia Olivella
- Departament de Biologia de Sistemes, Universitat de Vic, Vic, Barcelona 08500, Catalonia
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28
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Kaneko T, Huang H, Cao X, Li X, Li C, Voss C, Sidhu SS, Li SSC. Superbinder SH2 Domains Act as Antagonists of Cell Signaling. Sci Signal 2012; 5:ra68. [DOI: 10.1126/scisignal.2003021] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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29
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Kofler S, Asam C, Eckhard U, Wallner M, Ferreira F, Brandstetter H. Crystallographically mapped ligand binding differs in high and low IgE binding isoforms of birch pollen allergen bet v 1. J Mol Biol 2012; 422:109-23. [PMID: 22634284 PMCID: PMC3422537 DOI: 10.1016/j.jmb.2012.05.016] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 01/02/2023]
Abstract
The ability of pathogenesis-related proteins of family 10 to bind a broad spectrum of ligands is considered to play a key role for their physiological and pathological functions. In particular, Bet v 1, an archetypical allergen from birch pollen, is described as a highly promiscuous ligand acceptor. However, the detailed recognition mechanisms, including specificity factors discriminating binding properties of naturally occurring Bet v 1 variants, are poorly understood. Here, we report crystal structures of Bet v 1 variants in complex with an array of ligands at a resolution of up to 1.2 Å. Residue 30 within the hydrophobic pocket not only discriminates in high and low IgE binding Bet v 1 isoforms but also induces a drastic change in the binding mode of the model ligand deoxycholate. Ternary crystal structure complexes of Bet v 1 with several ligands together with the fluorogenic reporter 1-anilino-8-naphthalene sulfonate explain anomalous fluorescence binding curves obtained from 1-anilino-8-naphthalene sulfonate displacement assays. The structures reveal key interaction residues such as Tyr83 and rationalize both the binding specificity and promiscuity of the so-called hydrophobic pocket in Bet v 1. The intermolecular interactions of Bet v 1 reveal an unexpected complexity that will be indispensable to fully understand its roles within the physiological and allergenic context.
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Key Words
- ans, 1-anilino-8-naphthalene sulfonate
- bra, brassinolide
- dxc, deoxycholate
- idxc, inner deoxycholate
- odxc, outer deoxycholate
- lps, lipopolysaccharide
- mpd, 2-methyl-2,4-pentanediol
- ndsb-256, non-detergent sulfobetaine 256
- pr-10, pathogenesis-related protein 10
- pdb, protein data bank
- molecular allergenicity
- ans displacement assay
- structure–allergenicity relationship
- binding specificity and promiscuity
- dressed allergens
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Affiliation(s)
- Stefan Kofler
- Structural Biology Group, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Claudia Asam
- CD Laboratory for Allergy Diagnostics and Therapy, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Ulrich Eckhard
- Structural Biology Group, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Michael Wallner
- CD Laboratory for Allergy Diagnostics and Therapy, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Fátima Ferreira
- CD Laboratory for Allergy Diagnostics and Therapy, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Hans Brandstetter
- Structural Biology Group, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
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30
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Lundgren M, Niemi AJ, Sha F. Protein loops, solitons, and side-chain visualization with applications to the left-handed helix region. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061909. [PMID: 23005129 DOI: 10.1103/physreve.85.061909] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Indexed: 06/01/2023]
Abstract
Folded proteins have a modular assembly. They are constructed from regular secondary structures like α helices and β strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C_{α} atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C_{β} carbons on the two-sphere. We show that the residue independent localization extends to C_{γ} and C_{δ} carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed β turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.
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Affiliation(s)
- Martin Lundgren
- Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108 Uppsala, Sweden.
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31
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Alvarez LD, Mañez PA, Estrin DA, Burton G. The Caenorhabditis elegans DAF-12 nuclear receptor: structure, dynamics, and interaction with ligands. Proteins 2012; 80:1798-809. [PMID: 22489014 DOI: 10.1002/prot.24076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/13/2012] [Accepted: 03/18/2012] [Indexed: 11/08/2022]
Abstract
A structure for the ligand binding domain (LBD) of the DAF-12 receptor from Caenorhabditis elegans was obtained from the X-ray crystal structure of the receptor LBD from Strongyloides stercoralis bound to (25R)-Δ(7)-dafachronic acid (DA) (pdb:3GYU). The model was constructed in the presence of the ligand using a combination of Modeller, Autodock, and molecular dynamics (MD) programs, and then its dynamical behavior was studied by MD. A strong ligand binding mode (LBM) was found, with the three arginines in the ligand binding pocket (LBP) contacting the C-26 carboxylate group of the DA. The quality of the ceDAF-12 model was then evaluated by constructing several ligand systems for which the experimental activity is known. Thus, the dynamical behavior of the ceDAF-12 complex with the more active (25S)-Δ(7)-DA showed two distinct binding modes, one of them being energetically more favorable compared with the 25R isomer. Then the effect of the Arg564Cys and Arg598Met mutations on the (25R)-Δ(7)-DA binding was analyzed. The MD simulations showed that in the first case the complex was unstable, consistent with the lack of transactivation activity of (25R)-Δ(7)-DA in this mutant. Instead, in the case of the Arg598Met mutant, known to produce a partial loss of activity, our model predicted smaller effects on the LBM with a more stable MD trajectory. The model also showed that removal of the C-25 methyl does not impede the simultaneous strong interaction of the carboxylate with the three arginines, predicting that 27-nor-DAs are putative ceDAF-12 ligands.
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Affiliation(s)
- Lautaro D Alvarez
- Departamento de Química Orgánica and UMYMFOR, CONICET-UBA, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
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32
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Real space refinement of crystal structures with canonical distributions of electrons. Structure 2012; 19:1739-43. [PMID: 22153496 PMCID: PMC3234344 DOI: 10.1016/j.str.2011.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 09/28/2011] [Accepted: 10/10/2011] [Indexed: 11/21/2022]
Abstract
Recurring groups of atoms in molecules are surrounded by specific canonical distributions of electrons. Deviations from these distributions reveal unrealistic molecular geometries. Here, we show how canonical electron densities can be combined with classical electron densities derived from X-ray diffraction experiments to drive the real space refinement of crystal structures. The refinement process generally yields superior molecular models with reduced excess electron densities and improved stereochemistry without compromising the agreement between molecular models and experimental data.
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33
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Vasudev PG, Banerjee M, Ramakrishnan C, Balaram P. Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins. Proteins 2012; 80:991-1002. [PMID: 22228445 DOI: 10.1002/prot.24001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 10/26/2011] [Accepted: 11/14/2011] [Indexed: 11/06/2022]
Abstract
Short range side chain-backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution ≤ 1.5 Å). Hydrogen bonds involving residues i - 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (C(n), where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C(10)(CO(δ)(i) …NH(i + 2)), C(13)(CO(δ)(i) …NH(i + 3)) and C(17)(N(δ)H(i) …CO(i - 4)) structures. In contrast, Gln predominantly forms C(16)(CO(ε)(i) …NH(i - 3)), C(12)(N(ε)H(i) …CO(i - 2)), C(15)(N(ε)H(i) …CO(i - 3)) and C(18)(N(ε)H(i) …CO(i - 4)) motifs, with only the C(18) motif being analogous to the Asn C(17) structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone β-turns and α-turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain-backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered.
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Affiliation(s)
- Prema G Vasudev
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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34
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Minkara MS, Davis PH, Radhakrishnan ML. Multiple drugs and multiple targets: An analysis of the electrostatic determinants of binding between non-nucleoside HIV-1 reverse transcriptase inhibitors and variants of HIV-1 RT. Proteins 2011; 80:573-90. [DOI: 10.1002/prot.23221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/13/2011] [Accepted: 10/06/2011] [Indexed: 11/09/2022]
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35
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Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis. Nat Struct Mol Biol 2011; 18:1109-14. [PMID: 21947205 PMCID: PMC3191118 DOI: 10.1038/nsmb.2127] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/21/2011] [Indexed: 11/10/2022]
Abstract
Collagen constitutes one third of the body protein in humans, reflecting its extraordinary role in health and disease. Of similar importance, therefore, are the idiosyncratic proteases that nature evolved for collagen remodeling. Intriguingly, the most efficient collagenases are those that enable clostridial bacteria to colonize their host tissues, but despite intense studies, the structural and mechanistic basis of these enzymes has remained elusive. Here we present the crystal structure of collagenase G from Clostridium histolyticum at 2.55 Å resolution. By combining the structural data with enzymatic and mutagenesis studies, we derive a conformational two-state model of bacterial collagenolysis, in which the recognition and unraveling of collagen microfibrils into triple helices as well as the unwinding of the latter go hand in hand with collagenase opening and closing.
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36
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Eichinger A, Haneburger I, Koller C, Jung K, Skerra A. Crystal structure of the sensory domain of Escherichia coli CadC, a member of the ToxR-like protein family. Protein Sci 2011; 20:656-69. [PMID: 21308846 DOI: 10.1002/pro.594] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The membrane-integral transcriptional activator CadC comprises sensory and transcriptional regulatory functions within one polypeptide chain. Its C-terminal periplasmic domain, CadC(pd), is responsible for sensing of environmental pH as well as for binding of the feedback inhibitor cadaverine. Here we describe the crystal structure of CadC(pd) (residues 188-512) solved at a resolution of 1.8 Å via multiple wavelength anomalous dispersion (MAD) using a ReCl(6)(2-) derivative. CadC(pd) reveals a novel fold comprising two subdomains: an N-terminal subdomain dominated by a β-sheet in contact with three α-helices and a C-terminal subdomain formed by an eleven-membered α-helical bundle, which is oriented almost perpendicular to the helices in the first subdomain. Further to the native protein, crystal structures were also solved for its variants D471N and D471E, which show functionally different behavior in pH sensing. Interestingly, in the heavy metal derivative of CadC(pd) used for MAD phasing a ReCl(6)(2-) ion was found in a cavity located between the two subdomains. Amino acid side chains that coordinate this complex ion are conserved in CadC homologues from various bacterial species, suggesting a function of the cavity in the binding of cadaverine, which was supported by docking studies. Notably, CadC(pd) forms a homo-dimer in solution, which can be explained by an extended, albeit rather polar interface between two symmetry-related monomers in the crystal structure. The occurrence of several acidic residues in this region suggests protonation-dependent changes in the mode of dimerization, which could eventually trigger transcriptional activation by CadC in the bacterial cytoplasm.
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Affiliation(s)
- Andreas Eichinger
- Munich Center for Integrated Protein Science and Lehrstuhl für Biologische Chemie, Technische Universität München, Freising-Weihenstephan, Germany
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37
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Pan A, Chanda I, Chakrabarti J. Analysis of the genome and proteome composition of Bdellovibrio bacteriovorus: indication for recent prey-derived horizontal gene transfer. Genomics 2011; 98:213-22. [PMID: 21722725 DOI: 10.1016/j.ygeno.2011.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 05/18/2011] [Accepted: 06/14/2011] [Indexed: 10/18/2022]
Abstract
The genome/proteome composition of Bdellovibrio bacteriovorus, the predatory microorganism that preys on other Gram-negative bacteria, has been analyzed. The study elucidates that translational selection plays a major role in genome compositional variation with higher intensity compared to other deltaproteobacteria. Other sources of variations having relatively minor contributions are local GC-bias, horizontal gene transfer and strand-specific mutational bias. The study identifies a group of AT-rich genes with distinct codon composition that is presumably acquired by Bdellovibrio recently from Gram-negative prey-bacteria other than deltaproteobacteria. The proteome composition of this species is influenced by various physico-chemical factors, viz, alcoholicity, residue-charge, aromaticity and hydropathy. Cell-wall-surface-anchor-family (CSAPs) and transporter proteins with distinct amino acid composition and specific secondary-structure also contribute notably to proteome compositional variation. CSAPs, which are low molecular-weight, outer-membrane proteins with highly disordered secondary-structure, have preference toward polar-uncharged residues and cysteine that presumably help in prey-predator interaction by providing particular bonds of attachment.
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Affiliation(s)
- Archana Pan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry-605014, India.
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38
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Alvarez LD, Dansey MV, Martí MA, Bertucci PY, Di Chenna PH, Pecci A, Burton G. Biological activity and ligand binding mode to the progesterone receptor of A-homo analogues of progesterone. Bioorg Med Chem 2011; 19:1683-91. [DOI: 10.1016/j.bmc.2011.01.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/11/2011] [Accepted: 01/16/2011] [Indexed: 11/27/2022]
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39
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Beaudoin JD, Perreault JP. 5'-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res 2010; 38:7022-36. [PMID: 20571090 PMCID: PMC2978341 DOI: 10.1093/nar/gkq557] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experiments permitting an in-depth evaluation of the impact of G-quadruplexes as translational repressors. Sequences including potential G-quadruplexes were selected within nine distinct genes encoding proteins involved in various biological processes. Their abilities to fold into G-quadruplex structures in vitro were evaluated using circular dichroism, thermal denaturation and the novel use of in-line probing. Six sequences were observed to fold into G-quadruplex structures in vitro, all of which exhibited translational inhibition in cellulo when linked to a reporter gene. Sequence analysis, direct mutagenesis and subsequent experiments were performed in order to define the rules governing the folding of G-quadruplexes. In addition, the impact of single-nucleotide polymorphism was shown to be important in the formation of G-quadruplexes located within the 5'-untranslated region of an mRNA. In light of these results, clearly the 5'-UTR G-quadruplexes represent a class of translational repressors that is broadly distributed in the cell.
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Affiliation(s)
- Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC, J1H 5N4, Canada
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40
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Lu H, Goren AC, Zhan CG. Characterization of the structures of phosphodiesterase 10 binding with adenosine 3',5'-monophosphate and guanosine 3',5'-monophosphate by hybrid quantum mechanical/molecular mechanical calculations. J Phys Chem B 2010; 114:7022-8. [PMID: 20443609 PMCID: PMC2878663 DOI: 10.1021/jp911527y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum mechanical/molecular mechanical (QM/MM) geometry optimizations of the X-ray crystal structures of PDE10-AMP (PDB code 2OUN ) and PDE10-GMP (PDB code 2OUQ ) complexes have been performed to characterize the state of the AMP and GMP products, respectively. Results show that only one phosphate oxygen atom (O1) is protonated for both AMP and GMP product complexes. In addition, QM/MM calculations have resolved the orientation of the amide group of Gln726 in PDE10-GMP which was in conflict with the assignment of the guanine group of GMP in the X-ray crystal structure. Calculations reveal that the amide oxygen and nitrogen atom of Gln726 are rotated 180 degrees, resulting in two strong hydrogen bonds formed between the amide group of Gln726 and the guanine group of GMP. Binding free energy calculations for both QM/MM-optimized structures confirm the new conformational assignment of Gln726 in PDE10-GMP. The calculated binding free energy of the rotated structure is approximately 22 kcal/mol lower than the X-ray crystal assignment. The lower energy is mainly derived from the formation of two hydrogen bonds between the amide group of Gln726 and the guanine group of GMP. This implies that the orientation of the amide oxygen and nitrogen atoms in PDE10-AMP is different from PDE10-GMP. Finally, our results help to understand why PDE10 can hydrolyze both cAMP and cGMP.
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Affiliation(s)
- Haiting Lu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose Street, Lexington, KY 40536
| | - Alan C. Goren
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose Street, Lexington, KY 40536
- Division of Natural Sciences & Mathematics, Transylvania University, 300 North Broadway, Lexington, KY 40508
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose Street, Lexington, KY 40536
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41
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Zaborsky N, Brunner M, Wallner M, Himly M, Karl T, Schwarzenbacher R, Ferreira F, Achatz G. Antigen aggregation decides the fate of the allergic immune response. THE JOURNAL OF IMMUNOLOGY 2009; 184:725-35. [PMID: 19995902 DOI: 10.4049/jimmunol.0902080] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Previously, defined naturally occurring isoforms of allergenic proteins were classified as hypoallergens and therefore suggested as an agent for immunotherapy in the future. In this paper, we report for the first time the molecular background of hypoallergenicity by comparing the immunological behavior of hyperallergenic Betula verrucosa major Ag 1a (Bet v 1a) and hypoallergenic Bet v 1d, two isoforms of the major birch pollen allergen Betula verrucosa 1. Despite their cross-reactivity, Bet v 1a and Bet v 1d differ in their capacity to induce protective Ab responses in BALB/c mice. Both isoforms induced similar specific IgE levels, but only Bet v 1d expressed relevant titers of serum IgGs and IgAs. Interestingly, hypoallergenic Bet v 1d activated dendritic cells more efficiently, followed by the production of increased amounts of Th1- as well as Th2-type cytokines. Surprisingly, compared with Bet v 1a, Bet v 1d-immunized mice showed a decreased proliferation of regulatory T cells. Crystallographic studies and dynamic light scattering revealed that Bet v 1d demonstrated a high tendency to form disulfide-linked aggregates due to a serine to cysteine exchange at residue 113. We conclude that aggregation of Bet v 1d triggers the establishment of a protective Ab titer and supports a rationale for Bet v 1d being a promising candidate for specific immunotherapy of birch pollen allergy.
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Affiliation(s)
- Nadja Zaborsky
- Department of Molecular Biology, Christian Doppler Laboratory for Allergy Diagnosis and Therapy, University of Salzburg, Salzburg, Austria
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42
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Garzón D, Bond PJ, Faraldo-Gómez JD. Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens. Mol Immunol 2009; 47:253-60. [PMID: 19828201 DOI: 10.1016/j.molimm.2009.09.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 09/10/2009] [Indexed: 11/29/2022]
Abstract
CD1 proteins mediate the trafficking and presentation of a diverse range of lipid antigens to T-cell receptors, and thus play a key role in our adaptive immune system. Crystal structures of several CD1 isoforms reveal a highly conserved tertiary structure, but also great variability in the anatomy of their binding pockets, reflecting their distinct ligand specificity. The structure of one important member of the family, CD1c, remains unknown. CD1c is of great interest as it can present an unusual and potent lipid antigen, mannosyl-beta(1)-phosphomycoketide (MPM) from Mycobacterium tuberculosis, the causative agent of tuberculosis. CD1c has also been reported to present acetylated 12-amino-acid-long peptides (lipo-12), an observation with broad immunological implications but difficult to rationalize on structural grounds. To gain insights into the structural basis for the ligand specificity of CD1c, we have generated an atomic model of its binding domain using a detailed position-specific multiple-template homology modeling approach. This model reveals structural features unique to this isoform, particularly with regard to the so-called pocket F', which provide a compelling rationale for the ability of CD1c to bind not only branched alkyl chains such as in MPM, but also long lipopeptides comparable to those presented by MHC proteins. A model of CD1c with bound MPM was constructed and analyzed through molecular dynamics simulations, showing marked structural stability in the time-scale of 100 ns. A model of CD1c in complex with lipo-12 is also presented.
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Affiliation(s)
- Diana Garzón
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
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43
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Strohmeier GA, Sović T, Steinkellner G, Hartner FS, Andryushkova A, Purkarthofer T, Glieder A, Gruber K, Griengl H. Investigation of lipase-catalyzed Michael-type carbon–carbon bond formations. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.05.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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44
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Bayden AS, Fornabaio M, Scarsdale JN, Kellogg GE. Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT. J Comput Aided Mol Des 2009; 23:621-32. [PMID: 19554265 DOI: 10.1007/s10822-009-9270-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 01/22/2009] [Indexed: 10/20/2022]
Abstract
A public web server performing computational titration at the active site in a protein-ligand complex has been implemented. This calculation is based on the Hydropathic interaction noncovalent force field. From 3D coordinate data for the protein, ligand and bridging waters (if available), the server predicts the best combination of protonation states for each ionizable residue and/or ligand functional group as well as the Gibbs free energy of binding for the ionization-optimized protein-ligand complex. The 3D structure for the modified molecules is available as output. In addition, a graph depicting how this energy changes with acidity, i.e., as a function of added protons, can be obtained. This data may prove to be of use in preparing models for virtual screening and molecular docking. A few illustrative examples are presented. In beta secretase (2va7) computational titration flipped the amide groups of Gln12 and Asn37 and protonated a ligand amine yielding an improvement of 6.37 kcal mol(-1) in the protein-ligand binding score. Protonation of Glu139 in mutant HIV-1 reverse transcriptase (2opq) allows a water bridge between the protein and inhibitor that increases the protein-ligand interaction score by 0.16 kcal mol(-1). In human sialidase NEU2 complexed with an isobutyl ether mimetic inhibitor (2f11) computational titration suggested that protonating Glu218, deprotonating Arg237, flipping the amide bond on Tyr334, and optimizing the positions of several other polar protons would increase the protein-ligand interaction score by 0.71 kcal mol(-1).
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Affiliation(s)
- Alexander S Bayden
- Department of Medicinal Chemistry & Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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45
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Kirchmair J, Markt P, Distinto S, Schuster D, Spitzer GM, Liedl KR, Langer T, Wolber G. The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery. J Med Chem 2009; 51:7021-40. [PMID: 18975926 DOI: 10.1021/jm8005977] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johannes Kirchmair
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences, University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
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46
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Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes. Comput Biol Chem 2009; 33:137-48. [DOI: 10.1016/j.compbiolchem.2008.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 08/25/2008] [Indexed: 11/22/2022]
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47
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Liu A, Wang J, Lu Z, Yao L, Li Y, Yan H. Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effects. Chembiochem 2009; 9:2860-71. [PMID: 18973166 DOI: 10.1002/cbic.200800467] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The configuration and hydrogen-bonding network of side-chain amides in a 35 kDa protein were determined by measuring differential and trans-hydrogen-bond H/D isotope effects by using the isotopomer-selective (IS)-TROSY technique, which leads to a reliable recognition and correction of erroneous rotamers that are frequently found in protein structures. First, the differential two-bond isotope effects on carbonyl (13)C' shifts, which are defined as Delta(2)Delta(13)C'(ND) = (2)Delta(13)C'(ND(E))-(2)Delta(13)C'(ND(Z)), provide a reliable means for the configuration assignment for side-chain amides, because environmental effects (hydrogen bonds and charges, etc.) are greatly attenuated over the two bonds that separate the carbon and hydrogen atoms, and the isotope effects fall into a narrow range of positive values. Second and more importantly, the significant variations in the differential one-bond isotope effects on (15)N chemical shifts, which are defined as Delta(1)Delta(15)N(D) = (1)Delta(15)N(D(E))-(1)Delta(15)N(D(Z)) can be correlated with hydrogen-bonding interactions, particularly those involving charged acceptors. The differential one-bond isotope effects are additive, with major contributions from intrinsic differential conjugative interactions between the E and Z configurations, H-bonding interactions, and charge effects. Furthermore, the pattern of trans-H-bond H/D isotope effects can be mapped onto more complicated hydrogen-bonding networks that involve bifurcated hydrogen-bonds. Third, the correlations between Delta(1)Delta(15)N(D) and hydrogen-bonding interactions afford an effective means for the correction of erroneous rotamer assignments of side-chain amides. Rotamer correction by differential isotope effects is not only robust, but also simple and can be applied to large proteins.
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Affiliation(s)
- Aizhuo Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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48
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Weichenberger CX, Byzia P, Sippl MJ. Visualization of unfavorable interactions in protein folds. Bioinformatics 2008; 24:1206-7. [PMID: 18375963 DOI: 10.1093/bioinformatics/btn108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Three dimensional structures of proteins contain errors which often originate from limitations of the experimental techniques employed. Such errors frequently result in unfavorable atomic interactions. Here we present a new web service, called Interaction Viewer, for the visualization and correction of such errors. We show how the Interaction Viewer is used in combination with the NQ-Flipper service to spot strained asparagine and glutamine rotamers and we emphasize the convenience of this service in correcting such errors. AVAILABILITY The web service is integrated with the NQ-Flipper service and accessible at http://flipper.services.came.sbg.ac.at
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Affiliation(s)
- Christian X Weichenberger
- Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
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