101
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Mitchell LS, Colwell LJ. Comparative analysis of nanobody sequence and structure data. Proteins 2018; 86:697-706. [PMID: 29569425 PMCID: PMC6033041 DOI: 10.1002/prot.25497] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/25/2018] [Accepted: 03/20/2018] [Indexed: 02/04/2023]
Abstract
Nanobodies are a class of antigen‐binding protein derived from camelids that achieve comparable binding affinities and specificities to classical antibodies, despite comprising only a single 15 kDa variable domain. Their reduced size makes them an exciting target molecule with which we can explore the molecular code that underpins binding specificity—how is such high specificity achieved? Here, we use a novel dataset of 90 nonredundant, protein‐binding nanobodies with antigen‐bound crystal structures to address this question. To provide a baseline for comparison we construct an analogous set of classical antibodies, allowing us to probe how nanobodies achieve high specificity binding with a dramatically reduced sequence space. Our analysis reveals that nanobodies do not diversify their framework region to compensate for the loss of the VL domain. In addition to the previously reported increase in H3 loop length, we find that nanobodies create diversity by drawing their paratope regions from a significantly larger set of aligned sequence positions, and by exhibiting greater structural variation in their H1 and H2 loops.
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Affiliation(s)
- Laura S Mitchell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Lucy J Colwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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102
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Munikumar M, Krishna VS, Reddy VS, Rajeswari B, Sriram D, Rao MV. In silico design of small peptides antagonist against leptin receptor for the treatment of obesity and its associated immune-mediated diseases. J Mol Graph Model 2018; 82:20-36. [PMID: 29649778 DOI: 10.1016/j.jmgm.2018.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
Abstract
Excess adiposity in obese inhibits negatively impacts immune function and host defence. Obesity is characterized by a state of low-grade, chronic inflammation in addition to disturbed levels of circulating nutrients and metabolic hormones. The impact of metabolic abnormalities on obesity-related co-morbidities has undergone intense scrutiny over the past decades. Thus, treatment of obesity and its associated immune-mediated diseases is challenging due to impaired function of leptin system. These disorders are managed through antibiotics and by cytokines replacement. However, the effectiveness of cytokines coupled to the complexity of the cytokine network leads to severe side-effects, which can still occur after careful preclinical evaluation. In addition, synthetic immunotherapeutics carry a degree of risk, time-consuming and expensive. Hence, the complexity of existing therapy and adverse effects emphasizes the need for an alternative approach for the management of immune dysfunction associated with obesity. Computer-aided small molecule antibody technology has been successful in the design of novel biologicals for the diagnosis of diseases and therapeutic interventions. In this study, the crystal structure of leptin receptor (LEPR) complex with monoclonal antibody (9F8 Fab) was explored to predict Ag-Ab interactions using bioinformatics tools. The LEPR of complementarity-determining region (CDR) loops were mutated with published positive control residues of Ser, Thr, Tyr, Trp, and Phe to design a set of 678 peptides which were evaluated through Ag-peptide docking, binding free-energies, and interaction energies. Thus, hypothesized novel peptides can be explored as clinically applicable antagonists for the treatment of obesity and associated immune-mediated diseases.
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Affiliation(s)
- Manne Munikumar
- Biomedical Informatics Center (BMIC), National Institute of Nutrition, Indian Council of Medical Research (ICMR), Jamai-Osmania (Post), Hyderabad, 500007, Telangana, India.
| | - Vagolu Siva Krishna
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Ranga Reddy, 500078, India
| | | | - Bolla Rajeswari
- Biomedical Informatics Center (BMIC), National Institute of Nutrition, Indian Council of Medical Research (ICMR), Jamai-Osmania (Post), Hyderabad, 500007, Telangana, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Ranga Reddy, 500078, India
| | - Mendu Vishnuvardhana Rao
- National Institute of Medical Statistics, Indian Council of Medical Research, (ICMR), Ansari Nagar, New Delhi, 110029, India
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103
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Augustyniak D, Seredyński R, McClean S, Roszkowiak J, Roszniowski B, Smith DL, Drulis-Kawa Z, Mackiewicz P. Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross-reactive antibodies and have adapted during evolution. Sci Rep 2018; 8:4955. [PMID: 29563531 PMCID: PMC5862889 DOI: 10.1038/s41598-018-23029-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/05/2018] [Indexed: 12/31/2022] Open
Abstract
Moraxella catarrhalis is a common human respiratory tract pathogen. Its virulence factors associated with whole bacteria or outer membrane vesicles (OMVs) aid infection, colonization and may induce specific antibodies. To investigate pathogen-host interactions, we applied integrated bioinformatic and immunoproteomic (2D-electrophoresis, immunoblotting, LC-MS/MS) approaches. We showed that OMV proteins engaged exclusively in complement evasion and colonization strategies, but not those involved in iron transport and metabolism, are major targets for cross-reacting antibodies produced against phylogenetically divergent M. catarrhalis strains. The analysis of 31 complete genomes of M. catarrhalis and other Moraxella revealed that OMV protein-coding genes belong to 64 orthologous groups, five of which are restricted to M. catarrhalis. This species showed a two-fold increase in the number of OMV protein-coding genes relative to its ancestors and animal-pathogenic Moraxella. The appearance of specific OMV factors and the increase in OMV-associated virulence proteins during M. catarrhalis evolution is an interesting example of pathogen adaptation to optimize colonization. This precisely targeted cross-reactive immunity against M. catarrhalis may be an important strategy of host defences to counteract this phenomenon. We demonstrate that cross-reactivity is closely associated with the anti-virulent antibody repertoire which we have linked with adaptation of this pathogen to the host.
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Affiliation(s)
- Daria Augustyniak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
| | - Rafał Seredyński
- Department of Physiology, Wroclaw Medical University, T. Chalubinskiego 10, 50-368, Wroclaw, Poland.,Department of Physical Chemistry of Microorganisms, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, UCD O'Brien Centre for Science West, B304, Dublin, Ireland
| | - Justyna Roszkowiak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Bartosz Roszniowski
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Darren L Smith
- Applied Sciences, University of Northumbria, Ellison Building EBD222, Newcastle upon Tyne, NE1 8ST, UK
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383, Wrocław, Poland.
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104
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Zhao W, Pferdehirt L, Segatori L. Quantitatively Predictable Control of Cellular Protein Levels through Proteasomal Degradation. ACS Synth Biol 2018; 7:540-552. [PMID: 29061039 DOI: 10.1021/acssynbio.7b00325] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein function is typically studied and engineered by modulating protein levels within the complex cellular environment. To achieve fast, targeted, and predictable control of cellular protein levels without genetic manipulation of the target, we developed a technology for post-translational depletion based on a bifunctional molecule (NanoDeg) consisting of the antigen-binding fragment from the Camelidae species heavy-chain antibody (nanobody) fused to a degron signal that mediates degradation through the proteasome. We provide proof-of-principle demonstration of targeted degradation using a nanobody against the green fluorescent protein (GFP). Guided by predictive modeling, we show that customizing the NanoDeg rate of synthesis, rate of degradation, and mode of degradation enables quantitative and predictable control over the target's levels. Integrating the GFP-specific NanoDeg within a genetic circuit based on stimulus-dependent GFP output results in enhanced dynamic range and resolution of the output signal. By providing predictable control over cellular proteins' levels, the NanoDeg system could be readily used for a variety of systems-level analyses of cellular protein function.
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Affiliation(s)
- Wenting Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Lara Pferdehirt
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Laura Segatori
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
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105
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Ferhan AR, Jackman JA, Park JH, Cho NJ, Kim DH. Nanoplasmonic sensors for detecting circulating cancer biomarkers. Adv Drug Deliv Rev 2018; 125:48-77. [PMID: 29247763 DOI: 10.1016/j.addr.2017.12.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/29/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022]
Abstract
The detection of cancer biomarkers represents an important aspect of cancer diagnosis and prognosis. Recently, the concept of liquid biopsy has been introduced whereby diagnosis and prognosis are performed by means of analyzing biological fluids obtained from patients to detect and quantify circulating cancer biomarkers. Unlike conventional biopsy whereby primary tumor cells are analyzed, liquid biopsy enables the detection of a wide variety of circulating cancer biomarkers, including microRNA (miRNA), circulating tumor DNA (ctDNA), proteins, exosomes and circulating tumor cells (CTCs). Among the various techniques that have been developed to detect circulating cancer biomarkers, nanoplasmonic sensors represent a promising measurement approach due to high sensitivity and specificity as well as ease of instrumentation and operation. In this review, we discuss the relevance and applicability of three different categories of nanoplasmonic sensing techniques, namely surface plasmon resonance (SPR), localized surface plasmon resonance (LSPR) and surface-enhanced Raman scattering (SERS), for the detection of different classes of circulating cancer biomarkers.
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Affiliation(s)
- Abdul Rahim Ferhan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Joshua A Jackman
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jae Hyeon Park
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
| | - Dong-Hwan Kim
- School of Chemical Engineering, Sungkyunkwan University, 16419, Republic of Korea.
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106
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Cho E, Jung S. Biomolecule-Functionalized Smart Polydiacetylene for Biomedical and Environmental Sensing. Molecules 2018; 23:E107. [PMID: 29300355 PMCID: PMC6017116 DOI: 10.3390/molecules23010107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/22/2017] [Accepted: 12/29/2017] [Indexed: 02/02/2023] Open
Abstract
Polydiacetylene (PDA) has attracted interest for use as a sensing platform in biomedical, environmental, and chemical engineering applications owing to its capacity for colorimetric and fluorescent transition in response to external stimuli. Many researchers have attempted to develop a tailor-made PDA sensor via conjugation of chemical or biological substances to PDA. Here, we review smart bio-conjugates of PDA with various biomolecules such as carbohydrates, lipids, nucleic acids, and proteins. In addition, materialization and signal amplification strategies to improve handling and sensitivity are described.
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Affiliation(s)
- Eunae Cho
- Institute for Ubiquitous Information Technology and Applications (UBITA) & Center for Biotechnology Research in UBITA (CBRU), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
| | - Seunho Jung
- Department of Bioscience and Biotechnology, Microbial Carbohydrate Resource Bank (MBRC) & Center for Biotechnology Research in UBITA (CBRU), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
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107
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Feng T, Chen F, Kang Y, Sun H, Liu H, Li D, Zhu F, Hou T. HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. J Cheminform 2017; 9:66. [PMID: 29282565 PMCID: PMC5745212 DOI: 10.1186/s13321-017-0254-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/14/2017] [Indexed: 01/09/2023] Open
Abstract
Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for the structural modeling of PPIs, such as protein–protein docking, are quite needed to complement existing experimental techniques. The reliability of a protein–protein docking method is dependent on the ability of the scoring function to accurately distinguish the near-native binding structures from a huge number of decoys. In this study, we developed HawkRank, a novel scoring function designed for the sampling stage of protein–protein docking by summing the contributions from several energy terms, including van der Waals potentials, electrostatic potentials and desolvation potentials. First, based on the solvation free energies predicted by the Generalized Born model for ~ 800 proteins, a SASA (solvent accessible surface area)-based solvation model was developed, which can give the aqueous solvation free energies for proteins by summing the contributions of 21 atom types. Then, the van der Waals potentials and electrostatic potentials based on the Amber ff14SB force field were computed. Finally, the HawkRank scoring function was derived by determining the most optimal weights for five energy terms based on the training set. Here, MSR (modified success rate), a novel protein–protein scoring quality index, was used to assess the performance of HawkRank and three other popular protein–protein scoring functions, including ZRANK, FireDock and dDFIRE. The results show that HawkRank outperformed the other three scoring functions according to the total number of hits and MSR. HawkRank is available at http://cadd.zju.edu.cn/programs/hawkrank.
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Affiliation(s)
- Ting Feng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Fu Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China. .,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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108
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Lawson ADG, MacCoss M, Heer JP. Importance of Rigidity in Designing Small Molecule Drugs To Tackle Protein-Protein Interactions (PPIs) through Stabilization of Desired Conformers. J Med Chem 2017; 61:4283-4289. [PMID: 29140691 DOI: 10.1021/acs.jmedchem.7b01120] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Tackling PPIs, particularly by stabilizing clinically favored conformations of target proteins, with orally available, bona fide small molecules remains a significant but immensely worthwhile challenge for the pharmaceutical industry. Success may be more likely through the application of nature's learnings to build intrinsic rigidity into the design of clinical candidates.
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Affiliation(s)
| | - Malcolm MacCoss
- Bohicket Pharma Consulting LLC , 2556 Seabrook Island Road , Seabrook Island , South Carolina 29455 , United States
| | - Jag P Heer
- UCB , 216 Bath Road , Slough SL1 3WE , United Kingdom
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109
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Garza JA, Taylor AB, Sherwood LJ, Hart PJ, Hayhurst A. Unveiling a Drift Resistant Cryptotope within Marburgvirus Nucleoprotein Recognized by Llama Single-Domain Antibodies. Front Immunol 2017; 8:1234. [PMID: 29038656 PMCID: PMC5630700 DOI: 10.3389/fimmu.2017.01234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
Marburg virus (MARV) is a highly lethal hemorrhagic fever virus that is increasingly re-emerging in Africa, has been imported to both Europe and the US, and is also a Tier 1 bioterror threat. As a negative sense RNA virus, MARV has error prone replication which can yield progeny capable of evading countermeasures. To evaluate this vulnerability, we sought to determine the epitopes of 4 llama single-domain antibodies (sdAbs or VHH) specific for nucleoprotein (NP), each capable of forming MARV monoclonal affinity reagent sandwich assays. Here, we show that all sdAb bound the C-terminal region of NP, which was produced recombinantly to derive X-ray crystal structures of the three best performing antibody-antigen complexes. The common epitope is a trio of alpha helices that form a novel asymmetric basin-like depression that accommodates each sdAb paratope via substantial complementarity-determining region (CDR) restructuring. Shared core contacts were complemented by unique accessory contacts on the sides and overlooks of the basin yielding very different approach routes for each sdAb to bind the antigen. The C-terminal region of MARV NP was unable to be crystallized alone and required engagement with sdAb to form crystals suggesting the antibodies acted as crystallization chaperones. While gross structural homology is apparent between the two most conserved helices of MARV and Ebolavirus, the positions and morphologies of the resulting basins were markedly different. Naturally occurring amino acid variations occurring in bat and human Marburgvirus strains all mapped to surfaces distant from the predicted sdAb contacts suggesting a vital role for the NP interface in virus replication. As an essential internal structural component potentially interfacing with a partner protein it is likely the C-terminal epitope remains hidden or “cryptic” until virion disruption occurs. Conservation of this epitope over 50 years of Marburgvirus evolution should make these sdAb useful foundations for diagnostics and therapeutics resistant to drift.
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Affiliation(s)
- John Anthony Garza
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Alexander Bryan Taylor
- X-Ray Crystallography Core Laboratory, Department of Biochemistry and Structural Biology, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Laura Jo Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Peter John Hart
- X-Ray Crystallography Core Laboratory, Department of Biochemistry and Structural Biology, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX, United States
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
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110
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Fattahian Y, Riahi-Madvar A, Mirzaee R, Asadikaram G, Rahbar MR. In silico locating the immune-reactive segments of Lepidium draba peroxidase and designing a less immune-reactive enzyme derivative. Comput Biol Chem 2017; 70:21-30. [DOI: 10.1016/j.compbiolchem.2017.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 06/14/2017] [Accepted: 07/12/2017] [Indexed: 12/24/2022]
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111
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Tomita S, Ishihara S, Kurita R. A Multi-Fluorescent DNA/Graphene Oxide Conjugate Sensor for Signature-Based Protein Discrimination. SENSORS (BASEL, SWITZERLAND) 2017; 17:E2194. [PMID: 28946622 PMCID: PMC5677448 DOI: 10.3390/s17102194] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
Signature-based protein sensing has recently emerged as a promising prospective alternative to conventional lock-and-key methods. However, most of the current examples require the measurement of optical signals from spatially-separated materials for the generation of signatures. Herein, we present a new approach for the construction of multi-fluorescent sensing systems with high accessibility and tunability, which allows generating protein fluorescent signatures from a single microplate well. This approach is based on conjugates between nano-graphene oxide (nGO) and three single-stranded DNAs (ssDNAs) that exhibit different sequences and fluorophores. Initially, the three fluorophore-modified ssDNAs were quenched simultaneously by binding to nGO. Subsequent addition of analyte proteins caused a partial recovery in fluorescent intensity of the individual ssDNAs. Based on this scheme, we have succeeded in acquiring fluorescence signatures unique to (i) ten proteins that differ with respect to pI and molecular weight and (ii) biochemical marker proteins in the presence of interferent human serum. Pattern-recognition methods demonstrated high levels of discrimination for this system. The high discriminatory power and simple format of this sensor system should enable an easy and fast evaluation of proteins and protein mixtures.
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Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Sayaka Ishihara
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
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112
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Ren R, Zhang Y, Nadappuram BP, Akpinar B, Klenerman D, Ivanov AP, Edel JB, Korchev Y. Nanopore extended field-effect transistor for selective single-molecule biosensing. Nat Commun 2017; 8:586. [PMID: 28928405 PMCID: PMC5605549 DOI: 10.1038/s41467-017-00549-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/07/2017] [Indexed: 11/21/2022] Open
Abstract
There has been a significant drive to deliver nanotechnological solutions to biosensing, yet there remains an unmet need in the development of biosensors that are affordable, integrated, fast, capable of multiplexed detection, and offer high selectivity for trace analyte detection in biological fluids. Herein, some of these challenges are addressed by designing a new class of nanoscale sensors dubbed nanopore extended field-effect transistor (nexFET) that combine the advantages of nanopore single-molecule sensing, field-effect transistors, and recognition chemistry. We report on a polypyrrole functionalized nexFET, with controllable gate voltage that can be used to switch on/off, and slow down single-molecule DNA transport through a nanopore. This strategy enables higher molecular throughput, enhanced signal-to-noise, and even heightened selectivity via functionalization with an embedded receptor. This is shown for selective sensing of an anti-insulin antibody in the presence of its IgG isotype. Efficient detection of single molecules is vital to many biosensing technologies, which require analytical platforms with high selectivity and sensitivity. Ren et al. combine a nanopore sensor and a field-effect transistor, whereby gate voltage mediates DNA and protein transport through the nanopore.
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Affiliation(s)
- Ren Ren
- Department of Medicine, Imperial College London, London, W12 0NN, UK.,Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - Yanjun Zhang
- Department of Medicine, Imperial College London, London, W12 0NN, UK. .,Tianjin Neurological Institute, Tianjin Medical University General Hospital, Heping Qu, 300052, China.
| | | | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK.
| | - Yuri Korchev
- Department of Medicine, Imperial College London, London, W12 0NN, UK.,National University of Science & Technology MISIS, Moscow, 119049, Russia
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113
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Semi-synthetic vNAR libraries screened against therapeutic antibodies primarily deliver anti-idiotypic binders. Sci Rep 2017; 7:9676. [PMID: 28852148 PMCID: PMC5575089 DOI: 10.1038/s41598-017-10513-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023] Open
Abstract
Anti-idiotypic binders which specifically recognize the variable region of monoclonal antibodies have proven to be robust tools for pharmacokinetic studies of antibody therapeutics and for the development of cancer vaccines. In the present investigation, we focused on the identification of anti-idiotypic, shark-derived IgNAR antibody variable domains (vNARs) targeting the therapeutic antibodies matuzumab and cetuximab for the purpose of developing specific capturing ligands. Using yeast surface display and semi-synthetic, CDR3-randomized libraries, we identified several highly specific binders targeting both therapeutic antibodies in their corresponding variable region, without applying any counter selections during screening. Importantly, anti-idiotypic vNAR binders were not cross-reactive towards cetuximab or matuzumab, respectively, and comprised good target recognition in the presence of human and mouse serum. When coupled to magnetic beads, anti-idiotypic vNAR variants could be used as efficient capturing tools. Moreover, a two-step procedure involving vNAR-functionalized beads was employed for the enrichment of potentially bispecific cetuximab × matuzumab antibody constructs. In conclusion, semi-synthetic and CDR3-randomized vNAR libraries in combination with yeast display enable the fast and facile identification of anti-idiotypic vNAR domains targeting monoclonal antibodies primarily in an anti-idiotypic manner.
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114
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Wang D, Chai Y, Yuan Y, Yuan R. A Peptide Cleavage-Based Ultrasensitive Electrochemical Biosensor with an Ingenious Two-Stage DNA Template for Highly Efficient DNA Exponential Amplification. Anal Chem 2017; 89:8951-8956. [DOI: 10.1021/acs.analchem.7b01477] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ding Wang
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Chai
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yali Yuan
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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115
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Mariano R, Wuchty S. Structure-based prediction of host–pathogen protein interactions. Curr Opin Struct Biol 2017; 44:119-124. [DOI: 10.1016/j.sbi.2017.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/28/2017] [Indexed: 11/25/2022]
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116
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Maritan M, Cozzi R, Lo Surdo P, Veggi D, Bottomley MJ, Malito E. Crystal structures of human Fabs targeting the Bexsero meningococcal vaccine antigen NHBA. Acta Crystallogr F Struct Biol Commun 2017; 73:305-314. [PMID: 28580917 PMCID: PMC5458386 DOI: 10.1107/s2053230x17006021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/20/2017] [Indexed: 11/10/2022] Open
Abstract
Neisserial heparin-binding antigen (NHBA) is a surface-exposed lipoprotein from Neisseria meningitidis and is a component of the meningococcus B vaccine Bexsero. As part of a study to characterize the three-dimensional structure of NHBA and the molecular basis of the human immune response to Bexsero, the crystal structures of two fragment antigen-binding domains (Fabs) isolated from human monoclonal antibodies targeting NHBA were determined. Through a high-resolution analysis of the organization and the amino-acid composition of the CDRs, these structures provide broad insights into the NHBA epitopes recognized by the human immune system. As expected, these Fabs also show remarkable structural conservation, as shown by a structural comparison of 15 structures of apo Fab 10C3 which were obtained from crystals grown in different crystallization conditions and were solved while searching for a complex with a bound NHBA fragment or epitope peptide. This study also provides indirect evidence for the intrinsically disordered nature of two N-terminal regions of NHBA.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Bacterial/chemistry
- Antibodies, Bacterial/genetics
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Bacterial Outer Membrane Proteins/chemistry
- Bacterial Outer Membrane Proteins/genetics
- Bacterial Outer Membrane Proteins/immunology
- Binding Sites
- Carrier Proteins/chemistry
- Carrier Proteins/genetics
- Carrier Proteins/immunology
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HEK293 Cells
- Humans
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/genetics
- Intrinsically Disordered Proteins/chemistry
- Intrinsically Disordered Proteins/genetics
- Intrinsically Disordered Proteins/immunology
- Kinetics
- Meningitis, Meningococcal/immunology
- Meningitis, Meningococcal/microbiology
- Meningitis, Meningococcal/prevention & control
- Meningococcal Vaccines/chemistry
- Meningococcal Vaccines/immunology
- Models, Molecular
- Neisseria meningitidis/chemistry
- Neisseria meningitidis/immunology
- Peptides/chemical synthesis
- Peptides/chemistry
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
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117
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Replacing antibodies with modified DNA aptamers in vaccine potency assays. Vaccine 2017; 35:5495-5502. [PMID: 28433327 DOI: 10.1016/j.vaccine.2017.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 03/29/2017] [Accepted: 04/03/2017] [Indexed: 12/22/2022]
Abstract
Vaccine in vitro potency assays are vital regulatory tests that are used to confirm the presence and concentration of an antigen of interest in a form that directly or indirectly relates to protective activity in patients. Current assays come in many forms, but they almost exclusively use antibody reagents for selective detection of the target antigen. Antibodies provide specific recognition of vaccine antigens but also exhibit drawbacks such as stability limitations, cost, and lot-to-lot variation, which can make it challenging to maintain the reagent throughout the lifetime of the vaccine. We explored replacing antibodies with aptamers. Aptamers are macromolecules, such as nucleic acids, which can bind to their targets with high specificity and affinity, similar to that of antibodies. Some of the advantages of using aptamers over antibodies is that aptamers can be more stable, smaller, less expensive to produce, synthesized in vitro, and logistically easier to supply throughout the multi-decade lifespan of a commercial vaccine. We created modified DNA aptamers against the common vaccine carrier protein, CRM197. Several aptamers were discovered and one was chosen for further characterization. The binding kinetics of the aptamer revealed an off-rate 16-fold slower than anti-CRM197 antibodies used for comparison. The aptamers were more sensitive than available antibodies in some assay formats and comparable in others. The aptamer epitope was mapped to the receptor-binding domain of CRM197, a site adjacent to a known antibody binding site. These data address some key aspects for a path forward in replacing antibodies with aptamers for use as critical reagents in vaccine assays. We further highlight the possibility of using nucleic acid reagents to develop next generation potency assays.
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118
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O'Kennedy R, Fitzgerald S, Murphy C. Don't blame it all on antibodies – The need for exhaustive characterisation, appropriate handling, and addressing the issues that affect specificity. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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119
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van der Kant R, Karow-Zwick AR, Van Durme J, Blech M, Gallardo R, Seeliger D, Aßfalg K, Baatsen P, Compernolle G, Gils A, Studts JM, Schulz P, Garidel P, Schymkowitz J, Rousseau F. Prediction and Reduction of the Aggregation of Monoclonal Antibodies. J Mol Biol 2017; 429:1244-1261. [PMID: 28322916 PMCID: PMC5397608 DOI: 10.1016/j.jmb.2017.03.014] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/21/2022]
Abstract
Protein aggregation remains a major area of focus in the production of monoclonal antibodies. Improving the intrinsic properties of antibodies can improve manufacturability, attrition rates, safety, formulation, titers, immunogenicity, and solubility. Here, we explore the potential of predicting and reducing the aggregation propensity of monoclonal antibodies, based on the identification of aggregation-prone regions and their contribution to the thermodynamic stability of the protein. Although aggregation-prone regions are thought to occur in the antigen binding region to drive hydrophobic binding with antigen, we were able to rationally design variants that display a marked decrease in aggregation propensity while retaining antigen binding through the introduction of artificial aggregation gatekeeper residues. The reduction in aggregation propensity was accompanied by an increase in expression titer, showing that reducing protein aggregation is beneficial throughout the development process. The data presented show that this approach can significantly reduce liabilities in novel therapeutic antibodies and proteins, leading to a more efficient path to clinical studies.
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Affiliation(s)
- Rob van der Kant
- VIB Switch Laboratory, Herestraat 49, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PO 802, B-3000 Leuven, Belgium
| | - Anne R Karow-Zwick
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach/Riss, Germany
| | - Joost Van Durme
- VIB Switch Laboratory, Herestraat 49, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PO 802, B-3000 Leuven, Belgium
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach/Riss, Germany
| | - Rodrigo Gallardo
- VIB Switch Laboratory, Herestraat 49, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PO 802, B-3000 Leuven, Belgium
| | - Daniel Seeliger
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach/Riss, Germany
| | - Kerstin Aßfalg
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach/Riss, Germany
| | - Pieter Baatsen
- EM-platform VIB Bio Imaging Core, VIB-KU Leuven, Herestraat 49, B-3000 Leuven
| | - Griet Compernolle
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Herestraat 49, PO 820, B-3000 Leuven, Belgium
| | - Ann Gils
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Herestraat 49, PO 820, B-3000 Leuven, Belgium
| | - Joey M Studts
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach/Riss, Germany
| | - Patrick Schulz
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach/Riss, Germany
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach/Riss, Germany
| | - Joost Schymkowitz
- VIB Switch Laboratory, Herestraat 49, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PO 802, B-3000 Leuven, Belgium.
| | - Frederic Rousseau
- VIB Switch Laboratory, Herestraat 49, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PO 802, B-3000 Leuven, Belgium.
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120
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Gao ZZ, Lin RL, Bai D, Tao Z, Liu JX, Xiao X. Host-guest complexation of cucurbit[8]uril with two enantiomers. Sci Rep 2017; 7:44717. [PMID: 28300189 PMCID: PMC5353740 DOI: 10.1038/srep44717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/13/2017] [Indexed: 01/06/2023] Open
Abstract
Host-guest complexation of cucurbit[8]uril (Q[8]) with two enantiomers, D-3-(2-naphthyl)-alanine (D-NA) and L-3-(2-naphthyl)-alanine (L-NA), has been fully investigated. Experimental data indicate that double guests reside within the cavity of Q[8] in both aqueous solution and solid state, generating highly stable homoternary complexes D-NA2@Q[8] and L-NA2@Q[8].
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Affiliation(s)
- Zhong-Zheng Gao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, P. R. China
| | - Rui-Lian Lin
- College of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan 243002, P. R. China
| | - Dong Bai
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, P. R. China
| | - Zhu Tao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, P. R. China
| | - Jing-Xin Liu
- College of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan 243002, P. R. China
| | - Xin Xiao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, P. R. China
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121
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Sen A, Hsieh WC, Aguilar RC. The Information Content of Glutamine-Rich Sequences Define Protein Functional Characteristics. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2017; 105:385-393. [PMID: 32963411 PMCID: PMC7505158 DOI: 10.1109/jproc.2016.2613076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The presence of abnormally expanded glutamine (Q) repeats within specific proteins (e.g., huntingtin) are the well-established cause of several neurogenerative diseases, including Huntington disease and spinocerebellar ataxias. However, the impact of "expanded Q" stretches on the protein function is not well-understood, mostly due to lack of knowledge about the physiological role of Q repeats and the mechanism by which these repeats achieve functional-specificity. Indeed, is intriguing that regions with such low complexity (low information content) can display exquisite functional specificity. Prompting the question: where is this information stored? Applying biochemical/structural constraints and statistical analysis of protein composition we identified Q-rich (QR) regions present in coiled coils of yeast transcription factors and endocytic proteins. Our analysis indicated the existence of non-Q amino-acids differentially enriched or excluded from QR regions in one protein group versus the other. Importantly, when the non-Q amino-acids from an endocytic protein were exchanged by the ones enriched in QR from transcription factors, the resulting protein was unable to localize to the plasma membrane and was instead found in the nucleus. These results indicate that while QR repeats can efficiently engage in binding, the non-Q amino-acids provide essential specificity information. We speculate that coupling low complexity regions with information-intensive determinants might be a strategy used in many protein systems involved in different biological processes.
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Affiliation(s)
- Arpita Sen
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Current address, Dept. of Molecular & Cell Biology, University of California, Berkeley
| | - Wen-Chieh Hsieh
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - R. Claudio Aguilar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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122
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Hu R, Luan J, Kharasch ED, Singamaneni S, Morrissey JJ. Aromatic Functionality of Target Proteins Influences Monomer Selection for Creating Artificial Antibodies on Plasmonic Biosensors. ACS APPLIED MATERIALS & INTERFACES 2017; 9:145-151. [PMID: 27935290 PMCID: PMC5372381 DOI: 10.1021/acsami.6b12505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Natural antibodies used as biorecognition elements suffer from numerous shortcomings, such as limited chemical and environmental stability and cost. Artificial antibodies based on molecular imprinting are an attractive alternative to natural antibodies. We investigated the role of aromatic interactions in target recognition capabilities of artificial antibodies. Three proteins with different aromatic amino acid content were employed as model targets. Artificial antibodies were formed on nanostructures using combinations of silane monomers of varying aromatic functionality. We employed refractive index sensitivity of plasmonic nanostructures as a transduction platform for monitoring various steps in the imprinting process and to quantify the target recognition capabilities of the artificial antibodies. The sensitivity of the artificial antibodies with aromatic interactions exhibited a protein-dependent enhancement. Selectivity and sensitivity enhancement due to the presence of aromatic groups in imprinted polymer matrix was found to be higher for target proteins with higher aromatic amino acid content. Our results indicate that tailoring the monomer composition based on the amino acid content of the target protein can improve the sensitivity of plasmonic biosensors based on artificial antibodies without affecting the selectivity.
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Affiliation(s)
- Rong Hu
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
- Department of Anesthesiology, Shanghai Ninth Peoples Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jingyi Luan
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering
| | - Evan D. Kharasch
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- The Center for Clinical Pharmacology, St. Louis College of Pharmacy and Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
| | - Srikanth Singamaneni
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering
| | - Jeremiah J. Morrissey
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
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123
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Kwong PD, Chuang G, DeKosky BJ, Gindin T, Georgiev IS, Lemmin T, Schramm CA, Sheng Z, Soto C, Yang A, Mascola JR, Shapiro L. Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1. Immunol Rev 2017; 275:108-128. [PMID: 28133812 PMCID: PMC5516196 DOI: 10.1111/imr.12480] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Numerous antibodies have been identified from HIV-1-infected donors that neutralize diverse strains of HIV-1. These antibodies may provide the basis for a B cell-mediated HIV-1 vaccine. However, it has been unclear how to elicit similar antibodies by vaccination. To address this issue, we have undertaken an informatics-based approach to understand the genetic and immunologic processes controlling the development of HIV-1-neutralizing antibodies. As DNA sequencing comprises the fastest growing database of biological information, we focused on incorporating next-generation sequencing of B-cell transcripts to determine the origin, maturation pathway, and prevalence of broadly neutralizing antibody lineages (Antibodyomics1, 2, 4, and 6). We also incorporated large-scale robotic analyses of serum neutralization to identify and quantify neutralizing antibodies in donor cohorts (Antibodyomics3). Statistical analyses furnish another layer of insight (Antibodyomics5), with physical characteristics of antibodies and their targets through molecular dynamics simulations (Antibodyomics7) and free energy perturbation analyses (Antibodyomics8) providing information-rich output. Functional interrogation of individual antibodies (Antibodyomics9) and synthetic antibody libraries (Antibodyomics10) also yields multi-dimensional data by which to understand and improve antibodies. Antibodyomics, described here, thus comprise resolution-enhancing tools, which collectively embody an information-driven discovery engine aimed toward the development of effective B cell-based vaccines.
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Affiliation(s)
- Peter D. Kwong
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
| | - Gwo‐Yu Chuang
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Brandon J. DeKosky
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Tatyana Gindin
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center and Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTNUSA
| | - Thomas Lemmin
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCAUSA
| | - Chaim A. Schramm
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Zizhang Sheng
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Cinque Soto
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - An‐Suei Yang
- Genomics Research CenterAcademia SinicaTaipeiTaiwan
| | - John R. Mascola
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Lawrence Shapiro
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
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124
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Abstract
Sensing using specific and selective receptors provides two very different but complementary strategies. This Sensor Issues article will discuss the merits and challenges of specific sensors, and selective sensors based on synthetic arrays. We will examine where each has been successfully applied to a sensing challenge, and then look at how a combined approach could take elements of both to provide new sensor platforms.
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Affiliation(s)
- William J. Peveler
- Department
of Chemistry, University College London, London, WC1H 0AJ, United Kingdom
| | - Mahdieh Yazdani
- Department
of Chemistry, University of Massachusetts Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - Vincent M. Rotello
- Department
of Chemistry, University of Massachusetts Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
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125
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Sonzini S, Marcozzi A, Gubeli RJ, van der Walle CF, Ravn P, Herrmann A, Scherman OA. High Affinity Recognition of a Selected Amino Acid Epitope within a Protein by Cucurbit[8]uril Complexation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Silvia Sonzini
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Formulation Sciences, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | - Alessio Marcozzi
- Zernike Institute for Advanced Materials; Dept. of Polymer Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Raphael J. Gubeli
- Formulation Sciences, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | | | - Peter Ravn
- Antibody Discovery and Protein Engineering, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials; Dept. of Polymer Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Oren A. Scherman
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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126
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Sonzini S, Marcozzi A, Gubeli RJ, van der Walle CF, Ravn P, Herrmann A, Scherman OA. High Affinity Recognition of a Selected Amino Acid Epitope within a Protein by Cucurbit[8]uril Complexation. Angew Chem Int Ed Engl 2016; 55:14000-14004. [DOI: 10.1002/anie.201606763] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/18/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Silvia Sonzini
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Formulation Sciences, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | - Alessio Marcozzi
- Zernike Institute for Advanced Materials; Dept. of Polymer Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Raphael J. Gubeli
- Formulation Sciences, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | | | - Peter Ravn
- Antibody Discovery and Protein Engineering, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials; Dept. of Polymer Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Oren A. Scherman
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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127
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High throughput cytotoxicity screening of anti-HER2 immunotoxins conjugated with antibody fragments from phage-displayed synthetic antibody libraries. Sci Rep 2016; 6:31878. [PMID: 27550798 PMCID: PMC4994030 DOI: 10.1038/srep31878] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/29/2016] [Indexed: 02/07/2023] Open
Abstract
Immunotoxins are an important class of antibody-based therapeutics. The potency of the immunotoxins depends on the antibody fragments as the guiding modules targeting designated molecules on cell surfaces. Phage-displayed synthetic antibody scFv libraries provide abundant antibody fragment candidates as targeting modules for the immunoconjugates, but the discovery of optimally functional immunoconjugates is limited by the scFv-payload conjugation procedure. In this work, cytotoxicity screening of non-covalently assembled immunotoxins was developed in high throughput format to discover highly functional synthetic antibody fragments for delivering toxin payloads. The principles governing the efficiency of the antibodies as targeting modules have been elucidated from large volume of cytotoxicity data: (a) epitope and paratope of the antibody-based targeting module are major determinants for the potency of the immunotoxins; (b) immunotoxins with bivalent antibody-based targeting modules are generally superior in cytotoxic potency to those with corresponding monovalent targeting module; and (c) the potency of the immunotoxins is positively correlated with the densities of the cell surface antigen. These findings suggest that screening against the target cells with a large pool of antibodies from synthetic antibody libraries without the limitations of natural antibody responses can lead to optimal potency and minimal off-target toxicity of the immunoconjugates.
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128
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Avrameas S. Autopolyreactivity Confers a Holistic Role in the Immune System. Scand J Immunol 2016; 83:227-34. [PMID: 26808310 DOI: 10.1111/sji.12414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/10/2016] [Indexed: 12/20/2022]
Abstract
In this review, we summarize and discuss some key findings from the study of naturally occurring autoantibodies. The B-cell compartment of the immune system appears to recognize almost all endogenous and environmental antigens. This ability is accomplished principally through autopolyreactive humoral and cellular immune receptors. This extended autopolyreactivity (1) along immunoglobulin gene recombination contributes to the immune system's ability to recognize a very large number of self and non-self constituents; and (2) generates a vast immune network that creates communication channels between the organism's interior and exterior. Thus, the immune system continuously evolves depending on the internal and external stimuli it encounters. Furthermore, this far-reaching network's existence implies activities resembling those of classical biological factors or activities that modulate the function of other classical biological factors. A few such antibodies have already been found. Another important concept is that natural autoantibodies are highly dependent on the presence or absence of commensal microbes in the organism. These results are in line with past and recent findings showing the fundamental influence of the microbiota on proper immune system development, and necessitate the existence of a host-microbe homeostasis. This homeostasis requires that the participating humoral and cellular receptors are able to recognize self-antigens and commensal microbes without damaging them. Autopolyreactive immune receptors expressing low affinity for both types of antigens fulfil this role. The immune system appears to play a holistic role similar to that of the nervous system.
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Affiliation(s)
- S Avrameas
- Laboratory of Immunology, Hellenic Pasteur Institute, Athens, Greece
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129
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Yang ZH, Zhuo Y, Yuan R, Chai YQ. Highly Effective Protein Converting Strategy for Ultrasensitive Electrochemical Assay of Cystatin C. Anal Chem 2016; 88:5189-96. [DOI: 10.1021/acs.analchem.6b00210] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zhe-Han Yang
- Key Laboratory of Luminescence
and Real-Time Analytic Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ying Zhuo
- Key Laboratory of Luminescence
and Real-Time Analytic Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence
and Real-Time Analytic Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence
and Real-Time Analytic Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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130
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Kuroda D, Gray JJ. Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking. Bioinformatics 2016; 32:2451-6. [PMID: 27153634 DOI: 10.1093/bioinformatics/btw197] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 04/03/2016] [Indexed: 11/12/2022] Open
Abstract
MOTIVATIONS Characterizing protein-protein interfaces and the hydrogen bonds is a first step to better understand proteins' structures and functions toward high-resolution protein design. However, there are few large-scale surveys of hydrogen bonds of interfaces. In addition, previous work of shape complementarity of protein complexes suggested that lower shape complementarity in antibody-antigen interfaces is related to their evolutionary origin. RESULTS Using 6637 non-redundant protein-protein interfaces, we revealed peculiar features of various protein complex types. In contrast to previous findings, the shape complementarity of antibody-antigen interfaces resembles that of the other interface types. These results highlight the importance of hydrogen bonds during evolution of protein interfaces and rectify the prevailing belief that antibodies have lower shape complementarity. CONTACT jgray@jhu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Analytical and Physical Chemistry, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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131
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Verma R, Yadav M, Pradhan D, Bhuyan R, Aggarwal S, Nayek A, Jain AK. Probing binding mechanism of interleukin-6 and olokizumab: in silico design of potential lead antibodies for autoimmune and inflammatory diseases. J Recept Signal Transduct Res 2016; 36:601-616. [PMID: 26982101 DOI: 10.3109/10799893.2016.1147584] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated in silico to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen-antibody (Ag - Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag - Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.
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Affiliation(s)
- Rashi Verma
- a Biomedical Informatics Centre, National Institute of Pathology - ICMR , New Delhi , India and
| | - Monika Yadav
- a Biomedical Informatics Centre, National Institute of Pathology - ICMR , New Delhi , India and
| | - Dibyabhaba Pradhan
- a Biomedical Informatics Centre, National Institute of Pathology - ICMR , New Delhi , India and
| | - Rajabrata Bhuyan
- b Bioinformatics Infrastructure Facility, University of Kalyani , Kalyani, West Bengal , India
| | - Shweta Aggarwal
- a Biomedical Informatics Centre, National Institute of Pathology - ICMR , New Delhi , India and
| | - Arnab Nayek
- a Biomedical Informatics Centre, National Institute of Pathology - ICMR , New Delhi , India and
| | - Arun Kumar Jain
- a Biomedical Informatics Centre, National Institute of Pathology - ICMR , New Delhi , India and
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132
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Esmaielbeiki R, Krawczyk K, Knapp B, Nebel JC, Deane CM. Progress and challenges in predicting protein interfaces. Brief Bioinform 2016; 17:117-31. [PMID: 25971595 PMCID: PMC4719070 DOI: 10.1093/bib/bbv027] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/18/2015] [Indexed: 12/31/2022] Open
Abstract
The majority of biological processes are mediated via protein-protein interactions. Determination of residues participating in such interactions improves our understanding of molecular mechanisms and facilitates the development of therapeutics. Experimental approaches to identifying interacting residues, such as mutagenesis, are costly and time-consuming and thus, computational methods for this purpose could streamline conventional pipelines. Here we review the field of computational protein interface prediction. We make a distinction between methods which address proteins in general and those targeted at antibodies, owing to the radically different binding mechanism of antibodies. We organize the multitude of currently available methods hierarchically based on required input and prediction principles to provide an overview of the field.
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133
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Tung CP, Chen IC, Yu CM, Peng HP, Jian JW, Ma SH, Lee YC, Jan JT, Yang AS. Discovering neutralizing antibodies targeting the stem epitope of H1N1 influenza hemagglutinin with synthetic phage-displayed antibody libraries. Sci Rep 2015; 5:15053. [PMID: 26456860 PMCID: PMC4601012 DOI: 10.1038/srep15053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 09/15/2015] [Indexed: 11/09/2022] Open
Abstract
Broadly neutralizing antibodies developed from the IGHV1-69 germline gene are known to bind to the stem region of hemagglutinin in diverse influenza viruses but the sequence determinants for the antigen recognition, including neutralization potency and binding affinity, are not clearly understood. Such understanding could inform designs of synthetic antibody libraries targeting the stem epitope on hemagglutinin, leading to artificially designed antibodies that are functionally advantageous over antibodies from natural antibody repertoires. In this work, the sequence space of the complementarity determining regions of a broadly neutralizing antibody (F10) targeting the stem epitope on the hemagglutinin of a strain of H1N1 influenza virus was systematically explored; the elucidated antibody-hemagglutinin recognition principles were used to design a phage-displayed antibody library, which was then used to discover neutralizing antibodies against another strain of H1N1 virus. More than 1000 functional antibody candidates were selected from the antibody library and were shown to neutralize the corresponding strain of influenza virus with up to 7 folds higher potency comparing with the parent F10 antibody. The antibody library could be used to discover functionally effective antibodies against other H1N1 influenza viruses, supporting the notion that target-specific antibody libraries can be designed and constructed with systematic sequence-function information.
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Affiliation(s)
- Chao-Ping Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan 112.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan 115
| | - Shiou-Hwa Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jia-Tsrong Jan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
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134
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Futami J, Nonomura H, Kido M, Niidoi N, Fujieda N, Hosoi A, Fujita K, Mandai K, Atago Y, Kinoshita R, Honjo T, Matsushita H, Uenaka A, Nakayama E, Kakimi K. Sensitive Multiplexed Quantitative Analysis of Autoantibodies to Cancer Antigens with Chemically S-Cationized Full-Length and Water-Soluble Denatured Proteins. Bioconjug Chem 2015; 26:2076-84. [PMID: 26355635 DOI: 10.1021/acs.bioconjchem.5b00328] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Humoral immune responses against tumor-associated antigens (TAAs) or cancer/testis antigens (CTAs) aberrantly expressed in tumor cells are frequently observed in cancer patients. Recent clinical studies have elucidated that anticancer immune responses with increased levels of anti-TAA/CTA antibodies improve cancer survival rates. Thus, these antibody levels are promising biomarkers for diagnosing the efficiency of cancer immunotherapy. Full-length antigens are favored for detecting anti-TAA/CTA antibodies because candidate antigen proteins contain multiple epitopes throughout their structures. In this study, we developed a methodology to prepare purified water-soluble and full-length antigens by using cysteine sulfhydryl group cationization (S-cationization) chemistry. S-Cationized antigens can be prepared from bacterial inclusion bodies, and they exhibit improved protein solubility but preserved antigenicity. Anti-TAA/CTA antibodies detected in cancer patients appeared to recognize linear epitopes, as well as conformational epitopes, and because the frequency of cysteine side-residues on the epitope-paratope interface was low, any adverse effects of S-cationization were virtually negligible for antibody binding. Furthermore, S-cationized antigen-immobilized Luminex beads could be successfully used in highly sensitive quantitative-multiplexed assays. Indeed, patients with a more broadly induced serum anti-TAA/CTA antibody level showed improved progression-free survival after immunotherapy. The comprehensive anti-TAA/CTA assay system, which uses S-cationized full-length and water-soluble recombinant antigens, may be a useful diagnostic tool for assessing the efficiency of cancer immunotherapy.
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Affiliation(s)
- Junichiro Futami
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Hidenori Nonomura
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Momoko Kido
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Naomi Niidoi
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Nao Fujieda
- Medinet Co. Ltd. , Yokohama, Kanagawa 222-0033, Japan.,Department of Immunotherapeutics, The University of Tokyo Hospital , Tokyo 113-8655, Japan
| | - Akihiro Hosoi
- Medinet Co. Ltd. , Yokohama, Kanagawa 222-0033, Japan.,Department of Immunotherapeutics, The University of Tokyo Hospital , Tokyo 113-8655, Japan
| | - Kana Fujita
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Komako Mandai
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Yuki Atago
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Rie Kinoshita
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Tomoko Honjo
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University , Okayama 700-8530, Japan
| | - Hirokazu Matsushita
- Department of Immunotherapeutics, The University of Tokyo Hospital , Tokyo 113-8655, Japan
| | - Akiko Uenaka
- Faculty of Health and Welfare, Kawasaki University of Medical Welfare , Kurashiki, Okayama 701-0193, Japan
| | - Eiichi Nakayama
- Faculty of Health and Welfare, Kawasaki University of Medical Welfare , Kurashiki, Okayama 701-0193, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital , Tokyo 113-8655, Japan
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135
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Chen HS, Hou SC, Jian JW, Goh KS, Shen ST, Lee YC, You JJ, Peng HP, Kuo WC, Chen ST, Peng MC, Wang AHJ, Yu CM, Chen IC, Tung CP, Chen TH, Ping Chiu K, Ma C, Yuan Wu C, Lin SW, Yang AS. Predominant structural configuration of natural antibody repertoires enables potent antibody responses against protein antigens. Sci Rep 2015. [PMID: 26202883 PMCID: PMC5378893 DOI: 10.1038/srep12411] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Humoral immunity against diverse pathogens is rapidly elicited from natural antibody repertoires of limited complexity. But the organizing principles underlying the antibody repertoires that facilitate this immunity are not well-understood. We used HER2 as a model immunogen and reverse-engineered murine antibody response through constructing an artificial antibody library encoded with rudimentary sequence and structural characteristics learned from high throughput sequencing of antibody variable domains. Antibodies selected in vitro from the phage-displayed synthetic antibody library bound to the model immunogen with high affinity and specificities, which reproduced the specificities of natural antibody responses. We conclude that natural antibody structural repertoires are shaped to allow functional antibodies to be encoded efficiently, within the complexity limit of an individual antibody repertoire, to bind to diverse protein antigens with high specificity and affinity. Phage-displayed synthetic antibody libraries, in conjunction with high-throughput sequencing, can thus be designed to replicate natural antibody responses and to generate novel antibodies against diverse antigens.
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Affiliation(s)
- Hong-Sen Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Shin-Chen Hou
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jhih-Wei Jian
- 1] Genomics Research Center, Academia Sinica, Taipei, Taiwan 115 [2] Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan 112 [3] Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan 115
| | - King-Siang Goh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - San-Tai Shen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jhong-Jhe You
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Wen-Chih Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Shui-Tsung Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Ming-Chi Peng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Chih Yuan Wu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
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136
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Akiba H, Tsumoto K. Thermodynamics of antibody–antigen interaction revealed by mutation analysis of antibody variable regions. ACTA ACUST UNITED AC 2015; 158:1-13. [DOI: 10.1093/jb/mvv049] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/11/2015] [Indexed: 01/20/2023]
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137
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Smith LC, Leach DG, Blaylock BE, Ali OA, Urbach AR. Sequence-Specific, Nanomolar Peptide Binding via Cucurbit[8]uril-Induced Folding and Inclusion of Neighboring Side Chains. J Am Chem Soc 2015; 137:3663-9. [DOI: 10.1021/jacs.5b00718] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Lauren C. Smith
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - David G. Leach
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Brittney E. Blaylock
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Omar A. Ali
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Adam R. Urbach
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
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138
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Hu X, Dinu CZ. Analysis of affinities between specific biological ligands using atomic force microscopy. Analyst 2015; 140:8118-26. [PMID: 26525901 DOI: 10.1039/c5an01748c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used atomic force microscopy to rank the energetics of biomolecular recognition events of protein–ligand complexes.
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Affiliation(s)
- Xiao Hu
- West Virginia University
- Department of Chemical Engineering
- Morgantown
- USA
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