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Nawn D, Hassan SS, Redwan EM, Bhattacharya T, Basu P, Lundstrom K, Uversky VN. Unveiling the genetic tapestry: Rare disease genomics of spinal muscular atrophy and phenylketonuria proteins. Int J Biol Macromol 2024; 269:131960. [PMID: 38697430 DOI: 10.1016/j.ijbiomac.2024.131960] [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: 01/07/2024] [Revised: 03/30/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
Rare diseases, defined by their low prevalence, present significant challenges, including delayed detection, expensive treatments, and limited research. This study delves into the genetic basis of two noteworthy rare diseases in Saudi Arabia: Phenylketonuria (PKU) and Spinal Muscular Atrophy (SMA). PKU, resulting from mutations in the phenylalanine hydroxylase (PAH) gene, exhibits geographical variability and impacts intellectual abilities. SMA, characterized by motor neuron loss, is linked to mutations in the survival of motor neuron 1 (SMN1) gene. Recognizing the importance of unveiling signature genomics in rare diseases, we conducted a quantitative study on PAH and SMN1 proteins of multiple organisms by employing various quantitative techniques to assess genetic variations. The derived signature-genomics contributes to a deeper understanding of these critical genes, paving the way for enhanced diagnostics for disorders associated with PAH and SMN1.
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Affiliation(s)
- Debaleena Nawn
- Indian Research Institute for Integrated Medicine (IRIIM), Unsani, Howrah 711302, West Bengal, India.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, West Bengal, India.
| | - Elrashdy M Redwan
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.
| | - Tanishta Bhattacharya
- Developmental Genetics (Dept III), Max Planck Institute for Heart and Lung Research, Ludwigstrabe 43, 61231, Bad Nauheim, Germany.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein, 2000, South Africa; Adjunct Faculty, Woxsen School of Sciences, Woxsen University, Hyderabad 500 033, Telangana, India.
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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2
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Sari L, Bali S, Joachimiak LA, Lin MM. Hairpin trimer transition state of amyloid fibril. Nat Commun 2024; 15:2756. [PMID: 38553453 PMCID: PMC10980705 DOI: 10.1038/s41467-024-46446-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
Protein fibril self-assembly is a universal transition implicated in neurodegenerative diseases. Although fibril structure/growth are well characterized, fibril nucleation is poorly understood. Here, we use a computational-experimental approach to resolve fibril nucleation. We show that monomer hairpin content quantified from molecular dynamics simulations is predictive of experimental fibril formation kinetics across a tau motif mutant library. Hairpin trimers are predicted to be fibril transition states; one hairpin spontaneously converts into the cross-beta conformation, templating subsequent fibril growth. We designed a disulfide-linked dimer mimicking the transition state that catalyzes fibril formation, measured by ThT fluorescence and TEM, of wild-type motif - which does not normally fibrillize. A dimer compatible with extended conformations but not the transition-state fails to nucleate fibril at any concentration. Tau repeat domain simulations show how long-range interactions sequester this motif in a mutation-dependent manner. This work implies that different fibril morphologies could arise from disease-dependent hairpin seeding from different loci.
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Affiliation(s)
- Levent Sari
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Milo M Lin
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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3
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Nawn D, Hassan SS, Sil M, Ghosh A, Goswami A, Basu P, Dayhoff GW, Lundstrom K, Uversky VN. The distal-proximal relationships among the human moonlighting proteins: Evolutionary hotspots and Darwinian checkpoints. Int J Biol Macromol 2024; 259:128998. [PMID: 38176503 DOI: 10.1016/j.ijbiomac.2023.128998] [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: 10/14/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
Moonlighting proteins, known for their ability to perform multiple, often unrelated functions within a single polypeptide chain, challenge the traditional "one gene, one protein, one function" paradigm. As organisms evolved, their genomes remained relatively stable in size, but the introduction of post-translational modifications and sub-strategies like protein promiscuity and intrinsic disorder enabled multifunctionality. Enzymes, in particular, exemplify this phenomenon, engaging in unrelated processes alongside their primary catalytic roles. This study employs a systematic, quantitative informatics approach to shed light on human moonlighting protein sequences. Phylogenetic analyses of human moonlighting proteins are presented, elucidating the distal-proximal relationships among these proteins based on sequence-derived quantitative features. The findings unveil the captivating world of human moonlighting proteins, urging further investigations in the emerging field of moonlighting proteomics, with the potential for significant contributions to our understanding of multifunctional proteins and their roles in diverse cellular processes and diseases.
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Affiliation(s)
- Debaleena Nawn
- Biological Science Division, Indian Statistical Institute, 203 B.T Road, Kolkata, 700108, West Bengal, India; Indian Research Institute for Integrated Medicine (IRIIM), Unsani, Howrah, 711302, West Bengal, India.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, West Bengal, India.
| | - Moumita Sil
- Biological Science Division, Indian Statistical Institute, 203 B.T Road, Kolkata, 700108, West Bengal, India.
| | - Ankita Ghosh
- Biological Science Division, Indian Statistical Institute, 203 B.T Road, Kolkata, 700108, West Bengal, India.
| | - Arunava Goswami
- Biological Science Division, Indian Statistical Institute, 203 B.T Road, Kolkata, 700108, West Bengal, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, South Africa; Woxsen School of Sciences, Woxsen University, Hyderabad 500 033, Telangana, India.
| | - Guy W Dayhoff
- Department of Chemistry, University of South Florida, Tampa, FL 33612, USA.
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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4
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Mahmoudi N, Mohamed E, Dehnavi SS, Aguilar LMC, Harvey AR, Parish CL, Williams RJ, Nisbet DR. Calming the Nerves via the Immune Instructive Physiochemical Properties of Self-Assembling Peptide Hydrogels. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303707. [PMID: 38030559 PMCID: PMC10837390 DOI: 10.1002/advs.202303707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/22/2023] [Indexed: 12/01/2023]
Abstract
Current therapies for the devastating damage caused by traumatic brain injuries (TBI) are limited. This is in part due to poor drug efficacy to modulate neuroinflammation, angiogenesis and/or promoting neuroprotection and is the combined result of challenges in getting drugs across the blood brain barrier, in a targeted approach. The negative impact of the injured extracellular matrix (ECM) has been identified as a factor in restricting post-injury plasticity of residual neurons and is shown to reduce the functional integration of grafted cells. Therefore, new strategies are needed to manipulate the extracellular environment at the subacute phase to enhance brain regeneration. In this review, potential strategies are to be discussed for the treatment of TBI by using self-assembling peptide (SAP) hydrogels, fabricated via the rational design of supramolecular peptide scaffolds, as an artificial ECM which under the appropriate conditions yields a supramolecular hydrogel. Sequence selection of the peptides allows the tuning of these hydrogels' physical and biochemical properties such as charge, hydrophobicity, cell adhesiveness, stiffness, factor presentation, degradation profile and responsiveness to (external) stimuli. This review aims to facilitate the development of more intelligent biomaterials in the future to satisfy the parameters, requirements, and opportunities for the effective treatment of TBI.
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Affiliation(s)
- Negar Mahmoudi
- Laboratory of Advanced Biomaterials, the John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- ANU College of Engineering & Computer Science, Australian National University, Canberra, ACT, 2601, Australia
- The Graeme Clark Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Elmira Mohamed
- Laboratory of Advanced Biomaterials, the John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - Shiva Soltani Dehnavi
- Laboratory of Advanced Biomaterials, the John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- ANU College of Engineering & Computer Science, Australian National University, Canberra, ACT, 2601, Australia
| | - Lilith M Caballero Aguilar
- Laboratory of Advanced Biomaterials, the John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Graeme Clark Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Alan R Harvey
- School of Human Sciences, The University of Western Australia, and Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
| | - Clare L Parish
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Richard J Williams
- IMPACT, School of Medicine, Deakin University, Geelong, VIC, 3217, Australia
| | - David R Nisbet
- Laboratory of Advanced Biomaterials, the John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Graeme Clark Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Melbourne Medical School, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, VIC, 3010, Australia
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5
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Mahmoudi N, Wang Y, Moriarty N, Ahmed NY, Dehorter N, Lisowski L, Harvey AR, Parish CL, Williams RJ, Nisbet DR. Neuronal Replenishment via Hydrogel-Rationed Delivery of Reprogramming Factors. ACS NANO 2024; 18:3597-3613. [PMID: 38221746 DOI: 10.1021/acsnano.3c11337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The central nervous system's limited capacity for regeneration often leads to permanent neuronal loss following injury. Reprogramming resident reactive astrocytes into induced neurons at the site of injury is a promising strategy for neural repair, but challenges persist in stabilizing and accurately targeting viral vectors for transgene expression. In this study, we employed a bioinspired self-assembling peptide (SAP) hydrogel for the precise and controlled release of a hybrid adeno-associated virus (AAV) vector, AAVDJ, carrying the NeuroD1 neural reprogramming transgene. This method effectively mitigates the issues of high viral dosage at the target site, off-target delivery, and immunogenic reactions, enhancing the vector's targeting and reprogramming efficiency. In vitro, this vector successfully induced neuron formation, as confirmed by morphological, histochemical, and electrophysiological analyses. In vivo, SAP-mediated delivery of AAVDJ-NeuroD1 facilitated the trans-differentiation of reactive host astrocytes into induced neurons, concurrently reducing glial scarring. Our findings introduce a safe and effective method for treating central nervous system injuries, marking a significant advancement in regenerative neuroscience.
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Affiliation(s)
- Negar Mahmoudi
- Laboratory of Advanced Biomaterials, the John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
- ANU College of Engineering & Computer Science, Acton, ACT 2601, Australia
| | - Yi Wang
- The Graeme Clark Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Niamh Moriarty
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Noorya Y Ahmed
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
- The Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nathalie Dehorter
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
- The Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Australian Genome Therapeutics Centre, Children's Medical Research Institute and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, 04-141 Warsaw, Poland
| | - Alan R Harvey
- School of Human Sciences, The University of Western Australia, and Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Clare L Parish
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Richard J Williams
- The Graeme Clark Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- IMPACT, School of Medicine, Deakin University, Geelong, VIC 3217, Australia
| | - David R Nisbet
- Laboratory of Advanced Biomaterials, the John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
- The Graeme Clark Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Melbourne Medical School, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, VIC 3010, Australia
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6
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Braghetto A, Orlandini E, Baiesi M. Interpretable Machine Learning of Amino Acid Patterns in Proteins: A Statistical Ensemble Approach. J Chem Theory Comput 2023; 19:6011-6022. [PMID: 37552831 PMCID: PMC10500975 DOI: 10.1021/acs.jctc.3c00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Indexed: 08/10/2023]
Abstract
Explainable and interpretable unsupervised machine learning helps one to understand the underlying structure of data. We introduce an ensemble analysis of machine learning models to consolidate their interpretation. Its application shows that restricted Boltzmann machines compress consistently into a few bits the information stored in a sequence of five amino acids at the start or end of α-helices or β-sheets. The weights learned by the machines reveal unexpected properties of the amino acids and the secondary structure of proteins: (i) His and Thr have a negligible contribution to the amphiphilic pattern of α-helices; (ii) there is a class of α-helices particularly rich in Ala at their end; (iii) Pro occupies most often slots otherwise occupied by polar or charged amino acids, and its presence at the start of helices is relevant; (iv) Glu and especially Asp on one side and Val, Leu, Iso, and Phe on the other display the strongest tendency to mark amphiphilic patterns, i.e., extreme values of an effective hydrophobicity, though they are not the most powerful (non)hydrophobic amino acids.
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Affiliation(s)
- Anna Braghetto
- Department
of Physics and Astronomy, University of
Padova, Via Marzolo 8, 35131 Padua, Italy
- INFN,
Sezione di Padova, Via
Marzolo 8, 35131 Padua, Italy
| | - Enzo Orlandini
- Department
of Physics and Astronomy, University of
Padova, Via Marzolo 8, 35131 Padua, Italy
- INFN,
Sezione di Padova, Via
Marzolo 8, 35131 Padua, Italy
| | - Marco Baiesi
- Department
of Physics and Astronomy, University of
Padova, Via Marzolo 8, 35131 Padua, Italy
- INFN,
Sezione di Padova, Via
Marzolo 8, 35131 Padua, Italy
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7
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Feng F, Song X, Tan Z, Tu Y, Xiao L, Xie P, Ma Y, Sun X, Ma J, Rong L, He L. Cooperative assembly of a designer peptide and silk fibroin into hybrid nanofiber gels for neural regeneration after spinal cord injury. SCIENCE ADVANCES 2023; 9:eadg0234. [PMID: 37352345 PMCID: PMC10289662 DOI: 10.1126/sciadv.adg0234] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/17/2023] [Indexed: 06/25/2023]
Abstract
Local reconstruction of a permissive environment with biomaterials is a promising strategy to treat spinal cord injury (SCI). We reported a hybrid hydrogel fabricated from a small functional self-assembling peptide (F-SAP) and large silk fibroin (SF). The diffusion of SF micelles into F-SAP solution was driven by the dynamic synergy between osmotic pressure and F-SAP/SF electrostatic interactions, resulting in the rearrangement of SF micelles and the formation of rod-like filaments with axes nearly perpendicular to F-SAP nanofibers. Spectroscopy analysis, including circular dichroism, Raman and fluorescence, indicated conformation changes of SF from random coil to β sheet, which contributed to enhanced mechanical properties of the resultant hybrid hydrogel. Furthermore, the F-SAP/SF hybrid hydrogel coupled with controlled release of NT-3 provided a permissive environment for neural regeneration by providing nanofibrous substrates for regenerating axons, inflammatory modulation and remyelination, consequently resulting in improved locomotion and electrophysiological properties. This hydrogel could be used as a long-term stent in vivo for the treatment of SCI.
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Affiliation(s)
- Feng Feng
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Xiyong Song
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Zan Tan
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Yujie Tu
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Longyou Xiao
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Pengfei Xie
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yahao Ma
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiumin Sun
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Junwu Ma
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Limin Rong
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Liumin He
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
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8
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Jana P, Samanta K, Ehlers M, Zellermann E, Bäcker S, Stauber RH, Schmuck C, Knauer SK. Impact of Peptide Sequences on Their Structure and Function: Mimicking of Virus-Like Nanoparticles for Nucleic Acid Delivery. Chembiochem 2023; 24:e202200519. [PMID: 36314419 PMCID: PMC10099937 DOI: 10.1002/cbic.202200519] [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: 09/09/2022] [Revised: 10/30/2022] [Indexed: 01/05/2023]
Abstract
We rationally designed a series of amphiphilic hepta-peptides enriched with a chemically conjugated guanidiniocarbonylpyrrole (GCP) unit at the lysine side chain. All peptides are composed of polar (GCP) and non-polar (cyclohexyl alanine) residues but differ in their sequence periodicity, resulting in different secondary as well as supramolecular structures. CD spectra revealed the assembly of β-sheet-, α-helical and random structures for peptides 1, 2 and 3, respectively. Consequently, this enabled the formation of distinct supramolecular assemblies such as fibres, nanorod-like or spherical aggregates. Notably, all three cationic peptides are equipped with the anion-binding GCP unit and thus possess a nucleic acid-binding centre. However, only the helical (2) and the unstructured (3) peptide were able to assemble into small virus-like DNA-polyplexes and effectively deliver DNA into cells. Notably, as both peptides (2 and 3) were also capable of siRNA-delivery, they could be utilized to downregulate expression of the caner-relevant protein Survivin.
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Affiliation(s)
- Poulami Jana
- Department of Chemistry, Kaliachak College Sultanganj, Malda, 732201-, West Bengal, India
| | - Krishnananda Samanta
- Department of Chemistry, Balurghat College Dakshin Dinajpur, 733101-, West Bengal, India
| | - Martin Ehlers
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Elio Zellermann
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Sandra Bäcker
- Molecular Biology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Roland H Stauber
- Molecular and Cellular Oncology, ENT Department, University Mainz Medical Center, 55131, Mainz, Germany
| | - Carsten Schmuck
- Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Shirley K Knauer
- Molecular Biology, University of Duisburg-Essen, 45117, Essen, Germany
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9
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Burke PC, Park H, Subramaniam AR. A nascent peptide code for translational control of mRNA stability in human cells. Nat Commun 2022; 13:6829. [PMID: 36369503 PMCID: PMC9652226 DOI: 10.1038/s41467-022-34664-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
Stability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers mRNA destabilization. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended β strands in silico and in vitro slowdown ribosomes and reduce mRNA levels in vivo. The resulting nascent peptide code underlies the mRNA effects of hundreds of endogenous peptide sequences in the human proteome. Our work suggests an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.
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Affiliation(s)
- Phillip C. Burke
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA ,grid.34477.330000000122986657Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Heungwon Park
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - Arvind Rasi Subramaniam
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA ,grid.34477.330000000122986657Department of Microbiology, University of Washington, Seattle, WA 98195 USA
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10
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Blaber M. Variable and Conserved Regions of Secondary Structure in the β-Trefoil Fold: Structure Versus Function. Front Mol Biosci 2022; 9:889943. [PMID: 35517858 PMCID: PMC9062101 DOI: 10.3389/fmolb.2022.889943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
β-trefoil proteins exhibit an approximate C3 rotational symmetry. An analysis of the secondary structure for members of this diverse superfamily of proteins indicates that it is comprised of remarkably conserved β-strands and highly-divergent turn regions. A fundamental “minimal” architecture can be identified that is devoid of heterogenous and extended turn regions, and is conserved among all family members. Conversely, the different functional families of β-trefoils can potentially be identified by their unique turn patterns (or turn “signature”). Such analyses provide clues as to the evolution of the β-trefoil family, suggesting a folding/stability role for the β-strands and a functional role for turn regions. This viewpoint can also guide de novo protein design of β-trefoil proteins having novel functionality.
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Affiliation(s)
- Michael Blaber
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, United States
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11
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Chatterjee A, Reja A, Pal S, Das D. Systems chemistry of peptide-assemblies for biochemical transformations. Chem Soc Rev 2022; 51:3047-3070. [PMID: 35316323 DOI: 10.1039/d1cs01178b] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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12
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Theodoroula NF, Karavasili C, Vlasiou MC, Primikyri A, Nicolaou C, Chatzikonstantinou AV, Chatzitaki AT, Petrou C, Bouropoulos N, Zacharis CK, Galatou E, Sarigiannis Y, Fatouros DG, Vizirianakis IS. NGIWY-Amide: A Bioinspired Ultrashort Self-Assembled Peptide Gelator for Local Drug Delivery Applications. Pharmaceutics 2022; 14:133. [PMID: 35057029 PMCID: PMC8778326 DOI: 10.3390/pharmaceutics14010133] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 01/14/2023] Open
Abstract
Fibrillar structures derived from plant or animal origin have long been a source of inspiration for the design of new biomaterials. The Asn-Gly-Ile-Trp-Tyr-NH2 (NGIWY-amide) pentapeptide, isolated from the sea cucumber Apostichopus japonicus, which spontaneously self-assembles in water to form hydrogel, pertains to this category. In this study, we evaluated this ultra-short cosmetic bioinspired peptide as vector for local drug delivery applications. Combining nuclear magnetic resonance, circular dichroism, infrared spectroscopy, X-ray diffraction, and rheological studies, the synthesized pentapeptide formed a stiff hydrogel with a high β-sheet content. Molecular dynamic simulations aligned well with scanning electron and atomic-force microscopy studies, revealing a highly filamentous structure with the fibers adopting a helical-twisted morphology. Model dye localization within the supramolecular hydrogel provided insights on the preferential distribution of hydrophobic and hydrophilic compounds in the hydrogel network. That was further depicted in the diffusion kinetics of drugs differing in their aqueous solubility and molecular weight, namely, doxorubicin hydrochloride, curcumin, and octreotide acetate, highlighting its versatility as a delivery vector of both hydrophobic and hydrophilic compounds of different molecular weight. Along with the observed cytocompatibility of the hydrogel, the NGIWY-amide pentapeptide may offer new approaches for cell growth, drug delivery, and 3D bioprinting tissue-engineering applications.
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Affiliation(s)
- Nikoleta F. Theodoroula
- Department of Molecular Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Christina Karavasili
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (C.K.); (A.-T.C.); (D.G.F.)
| | - Manos C. Vlasiou
- Department of Life & Health Sciences, University of Nicosia, Nicosia 2417, Cyprus; (M.C.V.); (C.N.); (C.P.); (E.G.)
| | | | - Christia Nicolaou
- Department of Life & Health Sciences, University of Nicosia, Nicosia 2417, Cyprus; (M.C.V.); (C.N.); (C.P.); (E.G.)
| | - Alexandra V. Chatzikonstantinou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece;
| | - Aikaterini-Theodora Chatzitaki
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (C.K.); (A.-T.C.); (D.G.F.)
| | - Christos Petrou
- Department of Life & Health Sciences, University of Nicosia, Nicosia 2417, Cyprus; (M.C.V.); (C.N.); (C.P.); (E.G.)
| | - Nikolaos Bouropoulos
- Department of Materials Science, University of Patras, 26504 Patras, Greece;
- Foundation for Research and Technology Hellas, Institute of Chemical Engineering and High Temperature Chemical Processes, 26504 Patras, Greece
| | - Constantinos K. Zacharis
- Laboratory of Pharmaceutical Analysis, Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Eleftheria Galatou
- Department of Life & Health Sciences, University of Nicosia, Nicosia 2417, Cyprus; (M.C.V.); (C.N.); (C.P.); (E.G.)
| | - Yiannis Sarigiannis
- Department of Life & Health Sciences, University of Nicosia, Nicosia 2417, Cyprus; (M.C.V.); (C.N.); (C.P.); (E.G.)
| | - Dimitrios G. Fatouros
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (C.K.); (A.-T.C.); (D.G.F.)
| | - Ioannis S. Vizirianakis
- Department of Molecular Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Department of Life & Health Sciences, University of Nicosia, Nicosia 2417, Cyprus; (M.C.V.); (C.N.); (C.P.); (E.G.)
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13
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Ansari A, Ibrahim F, Haider MS, Aman A. In vitro application of bacteriocin produced by
Lactiplantibacillus plantarum
for the biopreservation of meat at refrigeration temperature. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Asma Ansari
- The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE) University of Karachi Karachi Pakistan
| | - Fariha Ibrahim
- Department of Biomedical Engineering Ziauddin University Karachi Pakistan
| | - Muhammad Samee Haider
- Food and Marine Resources Research Centre (FMRRC), Pakistan Council of Scientific and Industrial Research (PCSIR) Karachi Pakistan
| | - Afsheen Aman
- The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE) University of Karachi Karachi Pakistan
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14
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Pitz ME, Nukovic AM, Elpers MA, Alexander-Bryant AA. Factors Affecting Secondary and Supramolecular Structures of Self-Assembling Peptide Nanocarriers. Macromol Biosci 2021; 22:e2100347. [PMID: 34800001 DOI: 10.1002/mabi.202100347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Indexed: 01/12/2023]
Abstract
Self-assembling peptides are a popular vector for therapeutic cargo delivery due to their versatility, tunability, and biocompatibility. Accurately predicting secondary and supramolecular structures of self-assembling peptides is essential for de novo peptide design. However, computational modeling of such assemblies is not yet able to accurately predict structure formation for many peptide sequences. This review identifies patterns in literature between secondary and supramolecular structures, primary sequences, and applications to provide a guide for informed peptide design. An overview of peptide structures, their applications as nanocarriers, and analytical methods for characterizing secondary and supramolecular structure is examined. A top-down approach is then used to identify trends between peptide sequence and assembly structure from the current literature, including an analysis of the drivers at work, such as local and nonlocal sequence effects and solution conditions.
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Affiliation(s)
- Megan E Pitz
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Alexandra M Nukovic
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Margaret A Elpers
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Angela A Alexander-Bryant
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
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15
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Wang F, Gnewou O, Wang S, Osinski T, Zuo X, Egelman EH, Conticello VP. Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide. MATTER 2021; 4:3217-3231. [PMID: 34632372 PMCID: PMC8494133 DOI: 10.1016/j.matt.2021.06.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical devices. These peptide assemblies have also been used as models for understanding biological processes, such as the pathological formation of amyloid. We investigate the assembly of an octapeptide sequence, Ac-FKFEFKFE-NH2, motivated by prior studies that demonstrated that this amphipathic β strand peptide self-assembled into fibrils and biocompatible hydrogels. Using high-resolution cryoelectron microscopy (cryo-EM), we are able to determine the atomic structure for two different coexisting forms of the fibrils, containing four and five β sandwich protofilaments, respectively. Surprisingly, the inner walls in both forms are parallel β sheets, while the outer walls are antiparallel β sheets. Our results demonstrate the chaotic nature of peptide self-assembly and illustrate the importance of cryo-EM structural analysis to understand the complex phase behavior of these materials at near-atomic resolution.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: (E.H.E.), (V.P.C.)
| | - Vincent P. Conticello
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA 30322, USA
- Lead contact
- Correspondence: (E.H.E.), (V.P.C.)
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16
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Arias S, Amini S, Krüger JM, Bangert LD, Börner HG. Implementing Zn 2+ ion and pH-value control into artificial mussel glue proteins by abstracting a His-rich domain from preCollagen. SOFT MATTER 2021; 17:2028-2033. [PMID: 33596288 DOI: 10.1039/d0sm02118k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A His-rich domain of preCollagen-D found in byssal threads is derivatized with Cys and Dopa flanks to allow for mussel-inspired polymerization. Artificial mussel glue proteins are accessed that combine cysteinyldopa for adhesion with sequences for pH or Zn2+ induced β-sheet formation. The artificial constructs show strong adsorption to Al2O3, the resulting coatings tolerate hypersaline conditions and cohesion is improved by activating the β-sheet formation, that enhances E-modulus up to 60%.
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Affiliation(s)
- Sandra Arias
- Humboldt-Universität zu Berlin, Department of Chemistry, Laboratory for Organic Synthesis of Functional Systems, Brook-Taylor-Str. 2, Berlin D-12489, Germany.
| | - Shahrouz Amini
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Potsdam 14424, Germany
| | - Jana M Krüger
- Humboldt-Universität zu Berlin, Department of Chemistry, Laboratory for Organic Synthesis of Functional Systems, Brook-Taylor-Str. 2, Berlin D-12489, Germany.
| | - Lukas D Bangert
- Humboldt-Universität zu Berlin, Department of Chemistry, Laboratory for Organic Synthesis of Functional Systems, Brook-Taylor-Str. 2, Berlin D-12489, Germany.
| | - Hans G Börner
- Humboldt-Universität zu Berlin, Department of Chemistry, Laboratory for Organic Synthesis of Functional Systems, Brook-Taylor-Str. 2, Berlin D-12489, Germany.
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17
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Abstract
Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify k-mer periodicity and generate continuous tracks of k-mer periodicity over genomic loci of interest, such as regulatory elements. periodicDNA will facilitate investigation and improve understanding of how periodic DNA sequence features impact function.
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Affiliation(s)
- Jacques Serizay
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, CB2 1QN, UK
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18
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Dec R, Dzwolak W. Extremely Amyloidogenic Single-Chain Analogues of Insulin's H-Fragment: Structural Adaptability of an Amyloid Stretch. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12150-12159. [PMID: 32988199 PMCID: PMC7586408 DOI: 10.1021/acs.langmuir.0c01747] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Relatively short amino acid sequences often play a pivotal role in triggering protein aggregation leading to the formation of amyloid fibrils. In the case of insulin, various regions of A- and B-chains have been implicated as the most relevant to the protein's amyloidogenicity. Here, we focus on the highly amyloidogenic H-fragment of insulin comprising the disulfide-bonded N-terminal parts of both chains. Analysis of the aggregation behavior of single-chain peptide derivatives of the H-fragment suggests that the A-chain's part initiates the aggregation process while the disulfide-tethered B-chain reluctantly adapts to amyloid structure. Merging of both A- and B-parts into single-chain continuous peptides (A-B and B-A) results in extreme amyloidogenicity exceeding that of the double-chain H-fragment as reflected by almost instantaneous de novo fibrillization. Amyloid fibrils of A-B and B-A present distinct morphological and infrared traits and do not cross-seed insulin. Our study suggests that the N-terminal part of insulin's A-chain containing the intact Cys6-Cys11 intrachain disulfide bond may constitute insulin's major amyloid stretch which, through its bent conformation, enforces a parallel in-register alignment of β-strands. Comparison of the self-association behavior of H, A-B, and B-A peptides suggests that A-chain's N-terminal amyloid stretch is very versatile and adaptive to various structural contexts.
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19
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Charest N, Tro M, Bowers MT, Shea JE. Latent Models of Molecular Dynamics Data: Automatic Order Parameter Generation for Peptide Fibrillization. J Phys Chem B 2020; 124:8012-8022. [PMID: 32790375 DOI: 10.1021/acs.jpcb.0c05763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Variational autoencoders are artificial neural networks with the capability to reduce highly dimensional sets of data to smaller dimensional, latent representations. In this work, these models are applied to molecular dynamics simulations of the self-assembly of coarse-grained peptides to obtain a singled-valued order parameter for amyloid aggregation. This automatically learned order parameter is constructed by time-averaging the latent parametrizations of internal coordinate representations and compared to the nematic order parameter which is commonly used to study ordering of similar systems in literature. It is found that the latent space value provides more tailored insight into the aggregation mechanism's details, correctly identifying fibril formation in instances where the nematic order parameter fails to do so. A means is provided by which the latent space value can be analyzed so that the major contributing internal coordinates are identified, allowing for a direct interpretation of the latent space order parameter in terms of the behavior of the system. The latent model is found to be an effective and convenient way of representing the data from the dynamic ensemble and provides a means of reducing the dimensionality of a system whose scale exceeds molecular systems so-far considered with similar tools. This bypasses a need for researcher speculation on what elements of a system best contribute to summarizing major transitions and suggests latent models are effective and insightful when applied to large systems with a diversity of complex behaviors.
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Affiliation(s)
- Nathaniel Charest
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Michael Tro
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
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20
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The Structure of Amyloid Versus the Structure of Globular Proteins. Int J Mol Sci 2020; 21:ijms21134683. [PMID: 32630137 PMCID: PMC7370054 DOI: 10.3390/ijms21134683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/19/2022] Open
Abstract
The issue of changing the structure of globular proteins into an amyloid form is in the focus of researchers' attention. Numerous experimental studies are carried out, and mathematical models to define the essence of amyloid transformation are sought. The present work focuses on the issue of the hydrophobic core structure in amyloids. The form of ordering the hydrophobic core in globular proteins is described by a 3D Gaussian distribution analog to the distribution of hydrophobicity in a spherical micelle. Amyloid fibril is a ribbon-like micelle made up of numerous individual chains, each representing a flat structure. The distribution of hydrophobicity within a single chain included in the fibril describes the 2D Gaussian distribution. Such a description expresses the location of polar residues on a circle with a center with a high level of hydrophobicity. The presence of this type of order in the amyloid forms available in Preotin Data Bank (PDB) (both in proto- and superfibrils) is demonstrated in the present work. In this system, it can be assumed that the amyloid transformation is a chain transition from 3D Gauss ordering to 2D Gauss ordering. This means changing the globular structure to a ribbon-like structure. This observation can provide a simple mathematical model for simulating the amyloid transformation of proteins.
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21
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Davis LK. Intelligent Design of 14-3-3 Docking Proteins Utilizing Synthetic Evolution Artificial Intelligence (SYN-AI). ACS OMEGA 2019; 4:18948-18960. [PMID: 31763516 PMCID: PMC6868599 DOI: 10.1021/acsomega.8b03100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 07/10/2019] [Indexed: 05/13/2023]
Abstract
The ability to write DNA code from scratch will allow for the discovery of new and interesting chemistries as well as allowing the rewiring of cell signal pathways. Herein, we have utilized synthetic evolution artificial intelligence (SYN-AI) to intelligently design a set of 14-3-3 docking genes. SYN-AI engineers synthetic genes utilizing a parental gene as an evolution template. Wherein, evolution is fast-forwarded by transforming template gene sequences to DNA secondary and tertiary codes based upon gene hierarchical structural levels. The DNA secondary code allows identification of genomic building blocks across an orthologous sequence space comprising multiple genomes. Where, the DNA tertiary code allows engineering of supersecondary structures. SYN-AI constructed a library of 10 million genes that was reduced to three structurally functional 14-3-3 docking genes by applying natural selection protocols. Synthetic protein identity was verified utilizing Clustal Omega sequence alignments and Phylogeny.fr phylogenetic analysis. Wherein, we were able to confirm the three-dimensional structure utilizing I-TASSER and protein-ligand interactions utilizing COACH and Cofactor. The conservation of allosteric communications was confirmed utilizing elastic and anisotropic network models. Whereby, we utilized elNemo and ANM2.1 to confirm conservation of the 14-3-3 ζ amphipathic groove. Notably, to the best of our knowledge, we report the first 14-3-3 docking genes to be written from scratch.
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Affiliation(s)
- Leroy K. Davis
- Prairie
View A&M University, Cooperative Agricultural Research Center (CARC), 700 University Drive, Prairie
View, Texas 77446-0518, United States
- Gene
Evolution Project, LLC, Baton Rouge, Louisiana 70835, United States
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22
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Lamiable A, Bitard-Feildel T, Rebehmed J, Quintus F, Schoentgen F, Mornon JP, Callebaut I. A topology-based investigation of protein interaction sites using Hydrophobic Cluster Analysis. Biochimie 2019; 167:68-80. [PMID: 31525399 DOI: 10.1016/j.biochi.2019.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/11/2019] [Indexed: 01/20/2023]
Abstract
Hydrophobic clusters, as defined by Hydrophobic Cluster Analysis (HCA), are conditioned binary patterns, made of hydrophobic and non-hydrophobic positions, whose limits fit well those of regular secondary structures. They were proved to be useful for predicting secondary structures in proteins from the only information of a single amino acid sequence and have permitted to assess, in a comprehensive way, the leading role of binary patterns in secondary structure preference towards a particular state. Here, we considered the available experimental 3D structures of protein globular domains to enlarge our previously reported hydrophobic cluster database (HCDB), almost doubling the number of hydrophobic cluster species (each species being defined by a unique binary pattern) that represent the most frequent structural bricks encountered within protein globular domains. We then used this updated HCDB to show that the hydrophobic amino acids of discordant clusters, i.e. those less abundant clusters for which the observed secondary structure is in disagreement with the binary pattern preference of the species to which they belong, are more exposed to solvent and are more involved in protein interfaces than the hydrophobic amino acids of concordant clusters. As amino acid composition differs between concordant/discordant clusters, considering binary patterns may be used to gain novel insights into key features of protein globular domain cores and surfaces. It can also provide useful information on possible conformational plasticity, including disorder to order transitions.
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Affiliation(s)
- Alexis Lamiable
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Joseph Rebehmed
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France; Lebanese American University, Department of Computer Science and Mathematics, Beirut, Lebanon
| | - Flavien Quintus
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Françoise Schoentgen
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Jean-Paul Mornon
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005, Paris, France.
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23
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Toussi CA, Haddadnia J. Improving protein secondary structure prediction: the evolutionary optimized classification algorithms. Struct Chem 2019. [DOI: 10.1007/s11224-018-1271-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Crowet JM, Nasir MN, Dony N, Deschamps A, Stroobant V, Morsomme P, Deleu M, Soumillion P, Lins L. Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study. Int J Mol Sci 2018; 19:ijms19092772. [PMID: 30223492 PMCID: PMC6163580 DOI: 10.3390/ijms19092772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 11/16/2022] Open
Abstract
By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called "peptergents") have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with "peptergency" properties, called ADA8 and extensively described by Tao et al., is studied by molecular dynamic simulations for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamic simulations are here used to image this mechanism and provide further molecular details for the replacement of detergent molecules around the protein. In addition, we generalized this behavior by designing an amphipathic peptide with beta propensity, which was called ABZ12. Both peptides are able to surround the membrane protein and displace surfactant molecules. To our best knowledge, this is the first molecular mechanism proposed for "peptergency".
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Affiliation(s)
- Jean Marc Crowet
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Mehmet Nail Nasir
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Nicolas Dony
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Antoine Deschamps
- Institut des Sciences de la Vie, Université catholique de Louvain, 4-5 Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium.
| | - Vincent Stroobant
- Ludwig Institute for Cancer Research, de Duve Institute and Université Catholique de Louvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium.
| | - Pierre Morsomme
- Institut des Sciences de la Vie, Université catholique de Louvain, 4-5 Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium.
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Patrice Soumillion
- Institut des Sciences de la Vie, Université catholique de Louvain, 4-5 Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium.
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
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25
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Zhao Y, Zhu R, Song X, Ma Z, Chen S, Wu D, Liu F, Ouyang S, Zhang J, Ramakrishna S, Zhu X, He L. Assembly Pathway Selection of Designer Self-Assembling Peptide and Fabrication of Hierarchical Scaffolds for Neural Regeneration. ACS APPLIED MATERIALS & INTERFACES 2018; 10:26128-26141. [PMID: 30001104 DOI: 10.1021/acsami.8b10764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The self-assembling peptide (SAP) RADA 16-I has been modified with various functional motifs to improve its performances in biomedical applications. Nevertheless, the assembly mechanisms of designer functional RADA 16-I SAPs (F-SAPs) have not been clearly illustrated. The main problem is the difficulty in preparing a completely molecular aqueous solution of F-SAP. In the current study, we demonstrated that different procedures for preparing the F-SAP solution could result in the formation of different conformations and consequently micro/macroscopic morphologies. F-SAP was molecularly dissolved in an appropriate solvent, such as hexafluoroisopropanol (HFIP), as evidenced by random coil conformation characterized by circular dichroism spectroscopy and morphologies under transmission electron microscopy. The monomers were induced into monolayers when the F-SAP solution in HFIP was adsorbed on mica as observed by atomic force microscopy. However, nanoscaled filaments containing β-sheets dominated in the F-SAP aqueous solution, in which case water acted as a poor solvent of F-SAP. Furthermore, the results of molecular dynamics simulation implicated that water facilitated F-SAP aggregation, whereas HFIP inhibited it. The β-sheet assemblies formed in water exhibited a high kinetic stability and did not disassemble rapidly after the addition of HFIP. Our study indicated that selecting the right assembly pathway of F-SAP required for targeted functions, for example, delivery of hydrophobic drugs in aqueous conditions, could be achieved by optimizing the preparation protocol in addition to molecular design. Moreover, hierarchical scaffolds mimicking the natural extracellular matrix could be fabricated by the direct electrospinning of F-SAP molecular solution in HFIP and biodegradable polymer for applications in neural regeneration by promoting neural differentiation, neurite outgrowth, and synapse formation.
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Affiliation(s)
| | | | - Xiyong Song
- National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Zheng Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , P. R. China
| | | | | | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , P. R. China
| | - Songying Ouyang
- National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Jianguo Zhang
- Center for Biological Imaging, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Seeram Ramakrishna
- Department of Mechanical Engineering, Faculty of Engineering , National University of Singapore , Singapore 117576 , Singapore
| | - Xiaofeng Zhu
- Department of Chinese Medicine, The First Affiliated Hospital of Jinan University , Jinan University , Guangzhou 510632 , China
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Lampel A, Ulijn RV, Tuttle T. Guiding principles for peptide nanotechnology through directed discovery. Chem Soc Rev 2018; 47:3737-3758. [PMID: 29748676 DOI: 10.1039/c8cs00177d] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.
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Affiliation(s)
- A Lampel
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), New York, NY, USA.
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27
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Upadhyay A, Mishra A. Amyloids of multiple species: are they helpful in survival? Biol Rev Camb Philos Soc 2018; 93:1363-1386. [DOI: 10.1111/brv.12399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 01/13/2018] [Accepted: 01/18/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Arun Upadhyay
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan 342011 India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan 342011 India
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28
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Ronen M, Kalanoor BS, Oren Z, Ron I, Tischler YR, Gerber D. Characterization of peptides self-assembly by low frequency Raman spectroscopy. RSC Adv 2018; 8:16161-16170. [PMID: 35542205 PMCID: PMC9080252 DOI: 10.1039/c8ra01232f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/12/2018] [Indexed: 11/29/2022] Open
Abstract
Low Frequency Vibrational (LFV) modes of peptides and proteins are attributed to the lattice vibrations and are dependent on their structural organization and self-assembly. Studies taken in order to assign specific absorption bands in the low frequency range to self-assembly behavior of peptides and proteins have been challenging. Here we used a single stage Low Frequency Raman (LF-Raman) spectrometer to study a series of diastereomeric analogue peptides to investigate the effect of peptides self-assembly on the LF-Raman modes. The structural variation of the diastereomeric analogues resulted in distinct self-assembly groups, as confirmed by transmission electron microscopy (TEM) and dynamic light scattering (DLS) data. Using LF-Raman spectroscopy, we consistently observed discrete peaks for each of the self-assembly groups. The correlation between the spectral features and structural morphologies was further supported by principal component analysis (PCA). The LFV modes provide further information on the degrees of freedom of the entire peptide within the higher order organization, reflecting the different arrangement of its hydrogen bonding and hydrophobic interactions. Thus, our approach provides a simple and robust complementary method to structural characterization of peptides assemblies. Characterization of structural changes in peptide assemblies by low frequency Raman spectroscopy.![]()
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Affiliation(s)
- Maria Ronen
- Mina and Everard Goodman Faculty of Life Sciences
- Bar-Ilan University
- Ramat-Gan 5290002
- Israel
- Bar-Ilan Institute for Nanotechnology and Advanced Materials
| | - Basanth S. Kalanoor
- Department of Chemistry
- Bar-Ilan University
- Ramat-Gan 5290002
- Israel
- Bar-Ilan Institute for Nanotechnology and Advanced Materials
| | - Ziv Oren
- Department of Biotechnology
- Israel Institute for Biological Research
- Nes-Ziona 7410001
- Israel
| | - Izhar Ron
- Department of Physical Chemistry
- Israel Institute of Biological Research
- Nes-Ziona 7410001
- Israel
| | - Yaakov R. Tischler
- Department of Chemistry
- Bar-Ilan University
- Ramat-Gan 5290002
- Israel
- Bar-Ilan Institute for Nanotechnology and Advanced Materials
| | - Doron Gerber
- Mina and Everard Goodman Faculty of Life Sciences
- Bar-Ilan University
- Ramat-Gan 5290002
- Israel
- Bar-Ilan Institute for Nanotechnology and Advanced Materials
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29
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Richard M, Felten AS, Chrétien F, Averlant-Petit MC, Pellegrini-Moïse N. Synthesis and conformational studies of short mixed γ/α-glycopeptides based on sugar γ 3,3 -amino acids. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.10.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers. Proc Natl Acad Sci U S A 2017; 114:E7460-E7468. [PMID: 28831002 DOI: 10.1073/pnas.1620179114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
It is not known how life originated. It is thought that prebiotic processes were able to synthesize short random polymers. However, then, how do short-chain molecules spontaneously grow longer? Also, how would random chains grow more informational and become autocatalytic (i.e., increasing their own concentrations)? We study the folding and binding of random sequences of hydrophobic ([Formula: see text]) and polar ([Formula: see text]) monomers in a computational model. We find that even short hydrophobic polar (HP) chains can collapse into relatively compact structures, exposing hydrophobic surfaces. In this way, they act as primitive versions of today's protein catalysts, elongating other such HP polymers as ribosomes would now do. Such foldamer catalysts are shown to form an autocatalytic set, through which short chains grow into longer chains that have particular sequences. An attractive feature of this model is that it does not overconverge to a single solution; it gives ensembles that could further evolve under selection. This mechanism describes how specific sequences and conformations could contribute to the chemistry-to-biology (CTB) transition.
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31
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Disruption of drug-resistant biofilms using de novo designed short α-helical antimicrobial peptides with idealized facial amphiphilicity. Acta Biomater 2017; 57:103-114. [PMID: 28457962 DOI: 10.1016/j.actbio.2017.04.032] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 12/28/2022]
Abstract
The escalating threat of antimicrobial resistance has increased pressure to develop novel therapeutic strategies to tackle drug-resistant infections. Antimicrobial peptides have emerged as a promising class of therapeutics for various systemic and topical clinical applications. In this study, the de novo design of α-helical peptides with idealized facial amphiphilicities, based on an understanding of the pertinent features of protein secondary structures, is presented. Synthetic amphiphiles composed of the backbone sequence (X1Y1Y2X2)n, where X1 and X2 are hydrophobic residues (Leu or Ile or Trp), Y1 and Y2 are cationic residues (Lys), and n is the number repeat units (2 or 2.5 or 3), demonstrated potent broad-spectrum antimicrobial activities against clinical isolates of drug-susceptible and multi-drug resistant bacteria. Live-cell imaging revealed that the most selective peptide, (LKKL)3, promoted rapid permeabilization of bacterial membranes. Importantly, (LKKL)3 not only suppressed biofilm growth, but effectively disrupted mature biofilms after only 2h of treatment. The peptides (LKKL)3 and (WKKW)3 suppressed the production of LPS-induced pro-inflammatory mediators to levels of unstimulated controls at low micromolar concentrations. Thus, the rational design strategies proposed herein can be implemented to develop potent, selective and multifunctional α-helical peptides to eradicate drug-resistant biofilm-associated infections. STATEMENT OF SIGNIFICANCE Antimicrobial peptides (AMPs) are increasingly explored as therapeutics for drug-resistant and biofilm-related infections to help expand the size and quality of the current antibiotic pipeline in the face of mounting antimicrobial resistance. Here, synthetic peptides rationally designed based upon principles governing the folding of natural α-helical AMPs, comprising the backbone sequence (X1Y1Y2X2)n, and which assemble into α-helical structures with idealized facial amphiphilicity, is presented. These multifunctional peptide amphiphiles demonstrate high bacterial selectivity, promote the disruption of pre-formed drug-resistant biofilms, and effectively neutralize endotoxins at low micromolar concentrations. Overall, the design strategies presented here could provide a useful tool for developing therapeutic peptides with broad-ranging clinical applications from the treatment and prevention of drug-resistant biofilms to the neutralization of bacterial endotoxins.
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32
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Chan KH, Lee WH, Zhuo S, Ni M. Harnessing supramolecular peptide nanotechnology in biomedical applications. Int J Nanomedicine 2017; 12:1171-1182. [PMID: 28223805 PMCID: PMC5310635 DOI: 10.2147/ijn.s126154] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The harnessing of peptides in biomedical applications is a recent hot topic. This arises mainly from the general biocompatibility of peptides, as well as from the ease of tunability of peptide structure to engineer desired properties. The ease of progression from laboratory testing to clinical trials is evident from the plethora of examples available. In this review, we compare and contrast how three distinct self-assembled peptide nanostructures possess different functions. We have 1) nanofibrils in biomaterials that can interact with cells, 2) nanoparticles that can traverse the bloodstream to deliver its payload and also be bioimaged, and 3) nanotubes that can serve as cross-membrane conduits and as a template for nanowire formation. Through this review, we aim to illustrate how various peptides, in their various self-assembled nanostructures, possess great promise in a wide range of biomedical applications and what more can be expected.
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Affiliation(s)
| | - Wei Hao Lee
- Department of Chemistry, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Shuangmu Zhuo
- Fujian Provincial Key Laboratory for Photonics Technology, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, People’s Republic of China
| | - Ming Ni
- Fujian Provincial Key Laboratory for Photonics Technology, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, People’s Republic of China
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33
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Kouza M, Banerji A, Kolinski A, Buhimschi IA, Kloczkowski A. Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model. Phys Chem Chem Phys 2017; 19:2990-2999. [PMID: 28079198 PMCID: PMC5305032 DOI: 10.1039/c6cp07145g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Preeclampsia, a pregnancy-specific disorder, shares typical pathophysiological features with protein misfolding disorders including Alzheimer's disease. Characteristic for preeclampsia is the involvement of multiple proteins of which fragments of SERPINA1 and β-amyloid co-aggregate in urine and placenta of preeclamptic women. To explore the biophysical basis of this interaction, we investigated the multidimensional efficacy of the FVFLM sequence in SERPINA1, as a model inhibitory agent of β-amyloid aggregation. After studying the oligomerization of FVFLM peptides using all-atom molecular dynamics simulations with the GROMOS43a1 force field and explicit water, we report that FVFLM can aggregate and its aggregation is spontaneous with a remarkably faster rate than that recorded for KLVFF (aggregation "hot-spot" from β-amyloid). The fast kinetics of FVFLM aggregation was found to be driven primarily by core-like aromatic interactions originating from the anti-parallel orientation of complementarily uncharged strands. The conspicuously stable aggregation mechanism observed for FVFLM peptides is found not to conform to the popular 'dock-lock' scheme. We also found high propensity of FVFLM for KLVFF binding. When present, FVFLM disrupts the β-amyloid aggregation pathway and we propose that FVFLM-like peptides might be used to prevent the assembly of full-length Aβ or other pro-amyloidogenic peptides into amyloid fibrils.
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Affiliation(s)
- M Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. and Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA
| | - A Banerji
- Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA
| | - A Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - I A Buhimschi
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43215, USA and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
| | - A Kloczkowski
- Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
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34
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Verly RM, Resende JM, Junior EFC, de Magalhães MTQ, Guimarães CFCR, Munhoz VHO, Bemquerer MP, Almeida FCL, Santoro MM, Piló-Veloso D, Bechinger B. Structure and membrane interactions of the homodimeric antibiotic peptide homotarsinin. Sci Rep 2017; 7:40854. [PMID: 28102305 PMCID: PMC5244374 DOI: 10.1038/srep40854] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/16/2016] [Indexed: 01/12/2023] Open
Abstract
Antimicrobial peptides (AMPs) from amphibian skin are valuable template structures to find new treatments against bacterial infections. This work describes for the first time the structure and membrane interactions of a homodimeric AMP. Homotarsinin, which was found in Phyllomedusa tarsius anurans, consists of two identical cystine-linked polypeptide chains each of 24 amino acid residues. The high-resolution structures of the monomeric and dimeric peptides were determined in aqueous buffers. The dimer exhibits a tightly packed coiled coil three-dimensional structure, keeping the hydrophobic residues screened from the aqueous environment. An overall cationic surface of the dimer assures enhanced interactions with negatively charged membranes. An extensive set of biophysical data allowed us to establish structure-function correlations with antimicrobial assays against Gram-positive and Gram-negative bacteria. Although both peptides present considerable antimicrobial activity, the dimer is significantly more effective in both antibacterial and membrane biophysical assays.
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Affiliation(s)
- Rodrigo M. Verly
- Departamento de Química Universidade Federal de Minas Gerais, P.O.Box 486, 31270-901 Belo Horizonte, MG, Brazil
- Departamento de Química Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000 Diamantina, MG, Brazil
| | - Jarbas M. Resende
- Departamento de Química Universidade Federal de Minas Gerais, P.O.Box 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Eduardo F. C. Junior
- Departamento de Química Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000 Diamantina, MG, Brazil
| | - Mariana T. Q. de Magalhães
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, P.O.Box 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Carlos F. C. R. Guimarães
- Departamento de Química Universidade Federal de Minas Gerais, P.O.Box 486, 31270-901 Belo Horizonte, MG, Brazil
- Departamento de Química Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000 Diamantina, MG, Brazil
| | - Victor H. O. Munhoz
- Departamento de Química Universidade Federal de Minas Gerais, P.O.Box 486, 31270-901 Belo Horizonte, MG, Brazil
- Departamento de Química Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000 Diamantina, MG, Brazil
| | - Marcelo Porto Bemquerer
- Laboratório de Espectrometria de Massa, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) - Recursos Genéticos e Biotecnologia, Estação Parque Biológico, Final W5, Asa Norte, Brasília, DF, 70770-900, Brazil
| | - Fábio C. L. Almeida
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas – CNRMN, Instituto de Bioquimica Médica, Programa de Biologia Estrutural, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo M. Santoro
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, P.O.Box 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Dorila Piló-Veloso
- Departamento de Química Universidade Federal de Minas Gerais, P.O.Box 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France
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35
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Sun Y, Zhang Y, Tian L, Zhao Y, Wu D, Xue W, Ramakrishna S, Wu W, He L. Self-assembly behaviors of molecular designer functional RADA16-I peptides: influence of motifs, pH, and assembly time. ACTA ACUST UNITED AC 2016; 12:015007. [PMID: 27934778 DOI: 10.1088/1748-605x/12/1/015007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the current study, we present three designer self-assembling peptides (SAPs) by appending RADA 16-I with epitopes IKVAV, RGD, and YIGSR, which have different net charges and amphiphilic properties at neutral pH. The self-assembly of the designer SAPs is intensively investigated as a function of pH, canion type, and assembly time. The morphologies of the designer SAPs were studied by atomic force microscope. The secondary structure was investigated by circular dichroism. The dynamic viscoelasticity of designer SAP solutions was examined during titration with different alkaline reagents. Our study indicated that both electrostatic and hydrophilic/hydrophobic interactions of the motifs exhibited influences on the self-assembly, consequentially affecting the fiber morphologies and rheological properties. Moreover, NaOH induced a quicker assembly/reassembly of the designer SAPs than Tris because of its strong ionic strength. Therefore, our study gained comprehensive insight into the self-assembling mechanism as references for developing RADA 16-I-based functional SAPs.
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Affiliation(s)
- Yuqiao Sun
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, People's Republic of China. Contributed equally to this work
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36
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Jana P, Ehlers M, Zellermann E, Samanta K, Schmuck C. pH-Controlled Formation of a Stable β-Sheet and Amyloid-like Fibers from an Amphiphilic Peptide: The Importance of a Tailor-Made Binding Motif for Secondary Structure Formation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Poulami Jana
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Martin Ehlers
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Elio Zellermann
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Krishnananda Samanta
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Carsten Schmuck
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
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37
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Jana P, Ehlers M, Zellermann E, Samanta K, Schmuck C. pH-Controlled Formation of a Stable β-Sheet and Amyloid-like Fibers from an Amphiphilic Peptide: The Importance of a Tailor-Made Binding Motif for Secondary Structure Formation. Angew Chem Int Ed Engl 2016; 55:15287-15291. [DOI: 10.1002/anie.201608069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Poulami Jana
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Martin Ehlers
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Elio Zellermann
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Krishnananda Samanta
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Carsten Schmuck
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
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38
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Bemporad F, Ramazzotti M. From the Evolution of Protein Sequences Able to Resist Self-Assembly to the Prediction of Aggregation Propensity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:1-47. [PMID: 28109326 DOI: 10.1016/bs.ircmb.2016.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Folding of polypeptide chains into biologically active entities is an astonishingly complex process, determined by the nature and the sequence of residues emerging from ribosomes. While it has been long believed that evolution has pressed genomes so that specific sequences could adopt unique, functional three-dimensional folds, it is now clear that complex protein machineries act as quality control system and supervise folding. Notwithstanding that, events such as erroneous folding, partial folding, or misfolding are frequent during the life of a cell or a whole organism, and they can escape controls. One of the possible outcomes of this misbehavior is cross-β aggregation, a super secondary structure which represents the hallmark of self-assembled, well organized, and extremely ordered structures termed amyloid fibrils. What if evolution would have not taken into account such possibilities? Twenty years of research point toward the idea that, in fact, evolution has constantly supervised the risk of errors and minimized their impact. In this review we tried to survey the major findings in the amyloid field, trying to describe what the real pitfalls of protein folding are-from an evolutionary perspective-and how sequence and structural features have evolved to balance the need for perfect, dynamic, functionally efficient structures, and the detrimental effects implicit in the dangerous process of folding. We will discuss how the knowledge obtained from these studies has been employed to produce computational methods able to assess, predict, and discriminate the aggregation properties of protein sequences.
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Affiliation(s)
- F Bemporad
- Università degli Studi di Firenze, Firenze, Italy.
| | - M Ramazzotti
- Università degli Studi di Firenze, Firenze, Italy.
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39
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Wong YM, Masunaga H, Chuah JA, Sudesh K, Numata K. Enzyme-Mimic Peptide Assembly To Achieve Amidolytic Activity. Biomacromolecules 2016; 17:3375-3385. [PMID: 27642764 DOI: 10.1021/acs.biomac.6b01169] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid fibers are classified as a new generation of tunable bionanomaterials that exhibit new functions related to their distinctive characteristics, such as their universality, tunability, and stiffness. Here, we introduce the catalytic residues of serine protease into a peptide catalyst (PC) via an enzyme-mimic approach. The rational design of a repeating pattern of polar and nonpolar amino acids favors the conversion of the peptides into amyloid-like fibrils via self-assembly. Distinct fibrous morphologies have been observed at different pH values and temperatures, which indicates that different fibril packing schemes can be designed; hence, fibrillar peptides can be used to generate efficient artificial catalysts for amidolytic activities at mild pH values. The results of atomic force microscopy, Raman spectroscopy, and wide-angle X-ray scattering analyses are used to discuss and compare the fibril structure of a fibrillar PC with its amidolytic activity. The pH of the fibrillation reaction crucially affects the pKa of the side chains of the catalytic triads and is important for stable fibril formation. Temperature is another important parameter that controls the self-assembly of peptides into highly stacked and laminated morphologies. The morphology and stability of fibrils are crucial and represent important factors for demonstrating the capability of the peptides to exert amidolytic activity. The observed amidolytic activity of PC4, one of the PCs, was validated using an inhibition assay, which revealed that PC4 can perform enzyme-like amidolytic catalysis. These results provide insights into the potential use of designed peptides in the generation of efficient artificial enzymes.
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Affiliation(s)
- Yoke-Ming Wong
- Enzyme Research Team, RIKEN Center for Sustainable Resource Science , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan.,Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia , 11800, Minden, Penang, Malaysia
| | - Hiroyasu Masunaga
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Jo-Ann Chuah
- Enzyme Research Team, RIKEN Center for Sustainable Resource Science , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia , 11800, Minden, Penang, Malaysia
| | - Keiji Numata
- Enzyme Research Team, RIKEN Center for Sustainable Resource Science , 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan
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40
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Rebehmed J, Quintus F, Mornon JP, Callebaut I. The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis. Proteins 2016; 84:624-38. [DOI: 10.1002/prot.25012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Joseph Rebehmed
- CNRS UMR7590; Sorbonne Universités, Université Pierre Et Marie Curie-Paris6 - MNHN - IRD - IUC; Paris France
| | - Flavien Quintus
- CNRS UMR7590; Sorbonne Universités, Université Pierre Et Marie Curie-Paris6 - MNHN - IRD - IUC; Paris France
| | - Jean-Paul Mornon
- CNRS UMR7590; Sorbonne Universités, Université Pierre Et Marie Curie-Paris6 - MNHN - IRD - IUC; Paris France
| | - Isabelle Callebaut
- CNRS UMR7590; Sorbonne Universités, Université Pierre Et Marie Curie-Paris6 - MNHN - IRD - IUC; Paris France
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41
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Medina SH, Miller SE, Keim AI, Gorka AP, Schnermann MJ, Schneider JP. An Intrinsically Disordered Peptide Facilitates Non-Endosomal Cell Entry. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Scott H. Medina
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Stephen E. Miller
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Allison I. Keim
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Alexander P. Gorka
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Martin J. Schnermann
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
| | - Joel P. Schneider
- Chemical Biology Laboratory; National Cancer Institute; National Institutes of Health Fort Detrick; 376 Boyle Street Frederick MD 21702-1201 USA
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42
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Medina SH, Miller SE, Keim AI, Gorka AP, Schnermann MJ, Schneider JP. An Intrinsically Disordered Peptide Facilitates Non-Endosomal Cell Entry. Angew Chem Int Ed Engl 2016; 55:3369-72. [PMID: 26835878 DOI: 10.1002/anie.201510518] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/14/2015] [Indexed: 01/03/2023]
Abstract
Many cell-penetrating peptides (CPPs) fold at cell surfaces, adopting α- or β-structure that enable their intracellular transport. However, the same structural folds that facilitate cellular entry can also elicit potent membrane-lytic activity, limiting their use in delivery applications. Further, a distinct CPP can enter cells through many mechanisms, often leading to endosomal entrapment. Herein, we describe an intrinsically disordered peptide (CLIP6) that exclusively employs non-endosomal mechanisms to cross cellular membranes, while being remarkably biocompatible and serum-stable. We show that a single anionic glutamate residue is responsible for maintaining the disordered bioactive state of the peptide, defines its mechanism of cellular entry, and is central to its biocompatibility. CLIP6 can deliver membrane-impermeable cargo directly to the cytoplasm of cells, suggesting its broad utility for delivery of drug candidates limited by poor cell permeability and endosomal degradation.
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Affiliation(s)
- Scott H Medina
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Stephen E Miller
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Allison I Keim
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Alexander P Gorka
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Martin J Schnermann
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA
| | - Joel P Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health Fort Detrick, 376 Boyle Street, Frederick, MD, 21702-1201, USA.
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43
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Sun Y, Li W, Wu X, Zhang N, Zhang Y, Ouyang S, Song X, Fang X, Seeram R, Xue W, He L, Wu W. Functional Self-Assembling Peptide Nanofiber Hydrogels Designed for Nerve Degeneration. ACS APPLIED MATERIALS & INTERFACES 2016; 8:2348-59. [PMID: 26720334 DOI: 10.1021/acsami.5b11473] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Self-assembling peptide (SAP) RADA16-I (Ac-(RADA)4-CONH2) has been suffering from a main drawback associated with low pH, which damages cells and host tissues upon direct exposure. In this study, we presented a strategy to prepare nanofiber hydrogels from two designer SAPs at neutral pH. RADA16-I was appended with functional motifs containing cell adhesion peptide RGD and neurite outgrowth peptide IKVAV. The two SAPs were specially designed to have opposite net charges at neutral pH, the combination of which created a nanofiber hydrogel (-IKVAV/-RGD) characterized by significantly higher G' than G″ in a viscoelasticity examination. Circular dichroism, Fourier transform infrared spectroscopy, and Raman measurements were performed to investigate the secondary structure of the designer SAPs, indicating that both the hydrophobic/hydrophilic properties and electrostatic interactions of the functional motifs play an important role in the self-assembling behavior of the designer SAPs. The neural progenitor cells (NPCs)/stem cells (NSCs) fully embedded in the 3D-IKVAV/-RGD nanofiber hydrogel survived, whereas those embedded within the RADA 16-I hydrogel hardly survived. Moreover, the -IKVAV/-RGD nanofiber hydrogel supported NPC/NSC neuron and astrocyte differentiation in a 3D environment without adding extra growth factors. Studies of three nerve injury models, including sciatic nerve defect, intracerebral hemorrhage, and spinal cord transection, indicated that the designer -IKVAV/-RGD nanofiber hydrogel provided a more permissive environment for nerve regeneration than the RADA 16-I hydrogel. Therefore, we reported a new mechanism that might be beneficial for the synthesis of SAPs for in vitro 3D cell culture and nerve regeneration.
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Affiliation(s)
- Yuqiao Sun
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering, College of Life Science and Technology, Jinan University , Guangzhou, Guangdong, 510632, China
| | - Wen Li
- School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong , Pokfulam, Hong Kong SAR, 000000, PR China
| | - Xiaoli Wu
- School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong , Pokfulam, Hong Kong SAR, 000000, PR China
| | - Na Zhang
- Guangdong-Hongkong-Macau Institute of CNS Regeneration (GHMICR), Jinan University , Guangzhou, Guangdong, 510632, China
| | - Yongnu Zhang
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering, College of Life Science and Technology, Jinan University , Guangzhou, Guangdong, 510632, China
| | - Songying Ouyang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Xiyong Song
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Xinyu Fang
- School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong , Pokfulam, Hong Kong SAR, 000000, PR China
| | - Ramakrishna Seeram
- Guangdong-Hongkong-Macau Institute of CNS Regeneration (GHMICR), Jinan University , Guangzhou, Guangdong, 510632, China
- Center for Nanofibers and Nanotechnology, Department of Mechanical Engineering, Faculty of Engineering, National University of Singapore , Singapore , 117576
| | - Wei Xue
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering, College of Life Science and Technology, Jinan University , Guangzhou, Guangdong, 510632, China
| | - Liumin He
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering, College of Life Science and Technology, Jinan University , Guangzhou, Guangdong, 510632, China
- School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong , Pokfulam, Hong Kong SAR, 000000, PR China
| | - Wutian Wu
- School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong , Pokfulam, Hong Kong SAR, 000000, PR China
- Guangdong-Hongkong-Macau Institute of CNS Regeneration (GHMICR), Jinan University , Guangzhou, Guangdong, 510632, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong , Pokfulam, Hong Kong SAR, 000000, PR China
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Mangelschots J, Bibian M, Gardiner J, Waddington L, Van Wanseele Y, Van Eeckhaut A, Acevedo MMD, Van Mele B, Madder A, Hoogenboom R, Ballet S. Mixed α/β-Peptides as a Class of Short Amphipathic Peptide Hydrogelators with Enhanced Proteolytic Stability. Biomacromolecules 2016; 17:437-45. [DOI: 10.1021/acs.biomac.5b01319] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - James Gardiner
- CSIRO Manufacturing
Flagship, Bayview Avenue, Clayton, VIC 3169, Australia
| | - Lynne Waddington
- CSIRO Manufacturing
Flagship, Bayview Avenue, Clayton, VIC 3169, Australia
| | - Yannick Van Wanseele
- Department
of Pharmaceutical Chemistry and Drug Analysis, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Ann Van Eeckhaut
- Department
of Pharmaceutical Chemistry and Drug Analysis, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
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45
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Leo N, Shang Y, Yu JJ, Zeng X. Characterization of Self-Assembled Monolayers of Peptide Mimotopes of CD20 Antigen and Their Binding with Rituximab. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13764-13772. [PMID: 26609837 DOI: 10.1021/acs.langmuir.5b02605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
CD20, expressed in greater than 90% of B-lymphocytic lymphomas, is a target for antibody therapy. Rituximab is a chimeric therapeutic monoclonal antibody (mAb) against the protein CD20, allowing it to destroy B cells and to treat lymphoma, leukemia, transplant rejection, and autoimmune disorder. In this work, the binding of rituximab to self-assembled monolayers (SAMs) of peptide mimotopes of CD20 antigen was systematically characterized. Four peptide mimotopes of CD 20 antigen were selected from the literature and redesigned to allow their SAM immobilizations on gold electrodes through a peptide linker with cysteine. The bindings of these peptides with rituximab and control mAbs (trastuzumab and bevacizumab) were characterized by quartz crystal microbalance (QCM). Among the four peptide mimotopes initially selected, the peptide designated as CN-14 (CGSGSGSWPRWLEN) was the most selective and sensitive for rituximab binding. The CN-14 SAM was further characterized by ellipsometry and atomic force microscopy. The thickness of the CN-14 SAM film was approximately 32 Å, and the CN-14 SAM is suggested to be stabilized by a salt bridge of Arg-10 and Glu-13 between CN-14 peptides. The CN-14 salt bridge was evaluated by a series of modifications to the CN-14 peptide sequence and characterized by QCM. The CN-14 amide variant produced a better affinity to rituximab than CN-14 without a significant impact on selectivity. As the pKa of the Glu residue of CN-14 increased, the affinity of the SAM to rituximab increased, whereas the selectivity decreased. This was attributed to the weakening of the salt bridge between the CN-14 Arg-10 and Glu-13 at higher pKa values for Glu-13. Our study shows that peptide mimotopes have potential benefits in sensor applications, as the peptide-peptide interactions in the SAMs can be manipulated by the addition of functional groups to the peptide to influence the binding of target proteins.
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Affiliation(s)
- Norman Leo
- Chemistry Department, Oakland University , Rochester, Michigan 48309, United States
| | - Yuqin Shang
- Chemistry Department, Oakland University , Rochester, Michigan 48309, United States
| | - Jing-jiang Yu
- Nanotechnology Measurements Division, Agilent Technologies, Inc. , Chandler, Arizona 85226, United States
- Nanotechnology Systems Division, Hitachi High Technologies America, Inc. , Clarksburg, Maryland 20871, United States
| | - Xiangqun Zeng
- Chemistry Department, Oakland University , Rochester, Michigan 48309, United States
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46
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Huang YM, Banerjee S, Crone DE, Schenkelberg CD, Pitman DJ, Buck PM, Bystroff C. Toward Computationally Designed Self-Reporting Biosensors Using Leave-One-Out Green Fluorescent Protein. Biochemistry 2015; 54:6263-73. [PMID: 26397806 DOI: 10.1021/acs.biochem.5b00786] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Leave-one-out green fluorescent protein (LOOn-GFP) is a circularly permuted and truncated GFP lacking the nth β-strand element. LOO7-GFP derived from the wild-type sequence (LOO7-WT) folds and reconstitutes fluorescence upon addition of β-strand 7 (S7) as an exogenous peptide. Computational protein design may be used to modify the sequence of LOO7-GFP to fit a different peptide sequence, while retaining the reconstitution activity. Here we present a computationally designed leave-one-out GFP in which wild-type strand 7 has been replaced by a 12-residue peptide (HA) from the H5 antigenic region of the Thailand strain of H5N1 influenza virus hemagglutinin. The DEEdesign software was used to generate a sequence library with mutations at 13 positions around the peptide, coding for approximately 3 × 10(5) sequence combinations. The library was coexpressed with the HA peptide in E. coli and colonies were screened for in vivo fluorescence. Glowing colonies were sequenced, and one (LOO7-HA4) with 7 mutations was purified and characterized. LOO7-HA4 folds, fluoresces in vivo and in vitro, and binds HA. However, binding results in a decrease in fluorescence instead of the expected increase, caused by the peptide-induced dissociation of a novel, glowing oligomeric complex instead of the reconstitution of the native structure. Efforts to improve binding and recover reconstitution using in vitro evolution produced colonies that glowed brighter and matured faster. Two of these were characterized. One lost all affinity for the HA peptide but glowed more brightly in the unbound oligomeric state. The other increased in affinity to the HA peptide but still did not reconstitute the fully folded state. Despite failing to fold completely, peptide binding by computational design was observed and was improved by directed evolution. The ratio of HA to S7 binding increased from 0.0 for the wild-type sequence (no binding) to 0.01 after computational design (weak binding) and to 0.48 (comparable binding) after in vitro evolution. The novel oligomeric state is composed of an open barrel.
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Affiliation(s)
- Yao-Ming Huang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , San Francisco, California 94158, United States
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47
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Peptide-Induced Amyloid-Like Conformational Transitions in Proteins. INTERNATIONAL JOURNAL OF PEPTIDES 2015; 2015:723186. [PMID: 26435719 PMCID: PMC4578744 DOI: 10.1155/2015/723186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 12/12/2022]
Abstract
Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. The most common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can cause the conformational transitions in the protein. Short peptides which could be produced during the protein life cycle or which are encoded by short open reading frames can affect the protein conformation and function.
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48
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Holzgräfe C, Wallin S. Smooth functional transition along a mutational pathway with an abrupt protein fold switch. Biophys J 2015; 107:1217-1225. [PMID: 25185557 DOI: 10.1016/j.bpj.2014.07.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/25/2014] [Accepted: 07/01/2014] [Indexed: 10/24/2022] Open
Abstract
Recent protein design experiments have demonstrated that proteins can migrate between folds through the accumulation of substitution mutations without visiting disordered or nonfunctional points in sequence space. To explore the biophysical mechanism underlying such transitions we use a three-letter continuous protein model with seven atoms per amino acid to provide realistic sequence-structure and sequence-function mappings through explicit simulation of the folding and interaction of model sequences. We start from two 16-amino-acid sequences folding into an α-helix and a β-hairpin, respectively, each of which has a preferred binding partner with 35 amino acids. We identify a mutational pathway between the two folds, which features a sharp fold switch. By contrast, we find that the transition in function is smooth. Moreover, the switch in preferred binding partner does not coincide with the fold switch. Discovery of new folds in evolution might therefore be facilitated by following fitness slopes in sequence space underpinned by binding-induced conformational switching.
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Affiliation(s)
- Christian Holzgräfe
- Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics, Lund University, Lund, Sweden
| | - Stefan Wallin
- Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics, Lund University, Lund, Sweden.
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49
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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50
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Hicks TM, Verbeek CJR, Lay MC, Manley-Harris M. Changes to amino acid composition of bloodmeal after chemical oxidation. RSC Adv 2015. [DOI: 10.1039/c5ra10587k] [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] Open
Abstract
The effect of oxidative decolouring with peracetic acid on the physical and chemical characteristics of bloodmeal proteins was investigated by assessing protein solubility, molecular weight distribution and final amino acid composition.
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Affiliation(s)
- T. M. Hicks
- School of Engineering
- Faculty of Science and Engineering
- University of Waikato
- Hamilton 3240
- New Zealand
| | - C. J. R. Verbeek
- School of Engineering
- Faculty of Science and Engineering
- University of Waikato
- Hamilton 3240
- New Zealand
| | - M. C. Lay
- School of Engineering
- Faculty of Science and Engineering
- University of Waikato
- Hamilton 3240
- New Zealand
| | - M. Manley-Harris
- School of Science
- Faculty of Science and Engineering
- University of Waikato
- Hamilton 3240
- New Zealand
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