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Welsh JA, Goberdhan DCI, O'Driscoll L, Buzas EI, Blenkiron C, Bussolati B, Cai H, Di Vizio D, Driedonks TAP, Erdbrügger U, Falcon‐Perez JM, Fu Q, Hill AF, Lenassi M, Lim SK, Mahoney MG, Mohanty S, Möller A, Nieuwland R, Ochiya T, Sahoo S, Torrecilhas AC, Zheng L, Zijlstra A, Abuelreich S, Bagabas R, Bergese P, Bridges EM, Brucale M, Burger D, Carney RP, Cocucci E, Colombo F, Crescitelli R, Hanser E, Harris AL, Haughey NJ, Hendrix A, Ivanov AR, Jovanovic‐Talisman T, Kruh‐Garcia NA, Ku'ulei‐Lyn Faustino V, Kyburz D, Lässer C, Lennon KM, Lötvall J, Maddox AL, Martens‐Uzunova ES, Mizenko RR, Newman LA, Ridolfi A, Rohde E, Rojalin T, Rowland A, Saftics A, Sandau US, Saugstad JA, Shekari F, Swift S, Ter‐Ovanesyan D, Tosar JP, Useckaite Z, Valle F, Varga Z, van der Pol E, van Herwijnen MJC, Wauben MHM, Wehman AM, Williams S, Zendrini A, Zimmerman AJ, MISEV Consortium, Théry C, Witwer KW. Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles 2024; 13:e12404. [PMID: 38326288 PMCID: PMC10850029 DOI: 10.1002/jev2.12404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 02/09/2024] Open
Abstract
Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly.
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Affiliation(s)
- Joshua A. Welsh
- Translational Nanobiology Section, Laboratory of PathologyNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Deborah C. I. Goberdhan
- Nuffield Department of Women's and Reproductive HealthUniversity of Oxford, Women's Centre, John Radcliffe HospitalOxfordUK
| | - Lorraine O'Driscoll
- School of Pharmacy and Pharmaceutical SciencesTrinity College DublinDublinIreland
- Trinity Biomedical Sciences InstituteTrinity College DublinDublinIreland
- Trinity St. James's Cancer InstituteTrinity College DublinDublinIreland
| | - Edit I. Buzas
- Department of Genetics, Cell‐ and ImmunobiologySemmelweis UniversityBudapestHungary
- HCEMM‐SU Extracellular Vesicle Research GroupSemmelweis UniversityBudapestHungary
- HUN‐REN‐SU Translational Extracellular Vesicle Research GroupSemmelweis UniversityBudapestHungary
| | - Cherie Blenkiron
- Faculty of Medical and Health SciencesThe University of AucklandAucklandNew Zealand
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health SciencesUniversity of TurinTurinItaly
| | | | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and TherapeuticsCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Tom A. P. Driedonks
- Department CDL ResearchUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Uta Erdbrügger
- University of Virginia Health SystemCharlottesvilleVirginiaUSA
| | - Juan M. Falcon‐Perez
- Exosomes Laboratory, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- Metabolomics Platform, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- IKERBASQUE, Basque Foundation for ScienceBilbaoSpain
| | - Qing‐Ling Fu
- Otorhinolaryngology Hospital, The First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Extracellular Vesicle Research and Clinical Translational CenterThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Andrew F. Hill
- Institute for Health and SportVictoria UniversityMelbourneAustralia
| | - Metka Lenassi
- Faculty of MedicineUniversity of LjubljanaLjubljanaSlovenia
| | - Sai Kiang Lim
- Institute of Molecular and Cell Biology (IMCB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Paracrine Therapeutics Pte. Ltd.SingaporeSingapore
- Department of Surgery, YLL School of MedicineNational University SingaporeSingaporeSingapore
| | - Mỹ G. Mahoney
- Thomas Jefferson UniversityPhiladelphiaPennsylvaniaUSA
| | - Sujata Mohanty
- Stem Cell FacilityAll India Institute of Medical SciencesNew DelhiIndia
| | - Andreas Möller
- Chinese University of Hong KongHong KongHong Kong S.A.R.
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam Vesicle Center, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Susmita Sahoo
- Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Ana C. Torrecilhas
- Laboratório de Imunologia Celular e Bioquímica de Fungos e Protozoários, Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP) Campus DiademaDiademaBrazil
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Andries Zijlstra
- Department of PathologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- GenentechSouth San FranciscoCaliforniaUSA
| | - Sarah Abuelreich
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Reem Bagabas
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Paolo Bergese
- Department of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
- Center for Colloid and Surface Science (CSGI)FlorenceItaly
- National Center for Gene Therapy and Drugs based on RNA TechnologyPaduaItaly
| | - Esther M. Bridges
- Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Marco Brucale
- Consiglio Nazionale delle Ricerche ‐ Istituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFlorenceItaly
| | - Dylan Burger
- Kidney Research CentreOttawa Hopsital Research InstituteOttawaCanada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaCanada
- School of Pharmaceutical SciencesUniversity of OttawaOttawaCanada
| | - Randy P. Carney
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
| | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
| | - Federico Colombo
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Rossella Crescitelli
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical SciencesSahlgrenska Academy, University of GothenburgGothenburgSweden
- Wallenberg Centre for Molecular and Translational Medicine, Institute of Clinical SciencesSahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Edveena Hanser
- Department of BiomedicineUniversity Hospital BaselBaselSwitzerland
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | | | - Norman J. Haughey
- Departments of Neurology and PsychiatryJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and RepairGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Alexander R. Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Tijana Jovanovic‐Talisman
- Department of Cancer Biology and Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Nicole A. Kruh‐Garcia
- Bio‐pharmaceutical Manufacturing and Academic Resource Center (BioMARC)Infectious Disease Research Center, Colorado State UniversityFort CollinsColoradoUSA
| | - Vroniqa Ku'ulei‐Lyn Faustino
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Diego Kyburz
- Department of BiomedicineUniversity of BaselBaselSwitzerland
- Department of RheumatologyUniversity Hospital BaselBaselSwitzerland
| | - Cecilia Lässer
- Krefting Research Centre, Department of Internal Medicine and Clinical NutritionInstitute of Medicine at Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Kathleen M. Lennon
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine at Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Adam L. Maddox
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Elena S. Martens‐Uzunova
- Erasmus MC Cancer InstituteUniversity Medical Center Rotterdam, Department of UrologyRotterdamThe Netherlands
| | - Rachel R. Mizenko
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
| | - Lauren A. Newman
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Andrea Ridolfi
- Department of Physics and Astronomy, and LaserLaB AmsterdamVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Eva Rohde
- Department of Transfusion Medicine, University HospitalSalzburger Landeskliniken GmbH of Paracelsus Medical UniversitySalzburgAustria
- GMP Unit, Paracelsus Medical UniversitySalzburgAustria
- Transfer Centre for Extracellular Vesicle Theralytic Technologies, EV‐TTSalzburgAustria
| | - Tatu Rojalin
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCaliforniaUSA
- Expansion Therapeutics, Structural Biology and BiophysicsJupiterFloridaUSA
| | - Andrew Rowland
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Andras Saftics
- Department of Molecular Medicine, Beckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCaliforniaUSA
| | - Ursula S. Sandau
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Julie A. Saugstad
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Celer DiagnosticsTorontoCanada
| | - Simon Swift
- Waipapa Taumata Rau University of AucklandAucklandNew Zealand
| | - Dmitry Ter‐Ovanesyan
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMassachusettsUSA
| | - Juan P. Tosar
- Universidad de la RepúblicaMontevideoUruguay
- Institut Pasteur de MontevideoMontevideoUruguay
| | - Zivile Useckaite
- College of Medicine and Public HealthFlinders UniversityAdelaideAustralia
| | - Francesco Valle
- Consiglio Nazionale delle Ricerche ‐ Istituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFlorenceItaly
| | - Zoltan Varga
- Biological Nanochemistry Research GroupInstitute of Materials and Environmental Chemistry, Research Centre for Natural SciencesBudapestHungary
- Department of Biophysics and Radiation BiologySemmelweis UniversityBudapestHungary
| | - Edwin van der Pol
- Amsterdam Vesicle Center, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Biomedical Engineering and Physics, Amsterdam UMC, location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Laboratory of Experimental Clinical Chemistry, Amsterdam UMC, location AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Martijn J. C. van Herwijnen
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Marca H. M. Wauben
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | | | | | - Andrea Zendrini
- Department of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
- Center for Colloid and Surface Science (CSGI)FlorenceItaly
| | - Alan J. Zimmerman
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | | | - Clotilde Théry
- Institut Curie, INSERM U932PSL UniversityParisFrance
- CurieCoreTech Extracellular Vesicles, Institut CurieParisFrance
| | - Kenneth W. Witwer
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- EV Core Facility “EXCEL”, Institute for Basic Biomedical SciencesJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer's DiseaseJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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Gaillard M, Thuaire A, Nonglaton G, Agache V, Roupioz Y, Raillon C. Biosensing extracellular vesicles: contribution of biomolecules in affinity-based methods for detection and isolation. Analyst 2020; 145:1997-2013. [PMID: 31960838 DOI: 10.1039/c9an01949a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Extracellular Vesicles (EVs) are lipid vesicles secreted by cells that allow intercellular communication. They are decorated with surface proteins, which are membrane proteins that can be targeted by biochemical techniques to isolate EVs from background particles. EVs have recently attracted attention for their potential applications as biomarkers for numerous diseases. This review focuses on the contribution of biomolecules used as ligands in affinity-based biosensors for the detection and isolation of EVs. Capturing biological objects like EVs with antibodies is well described in the literature through different biosensing techniques. However, since handling proteins can be challenging due to stability issues, sensors using non-denaturable biomolecules are emerging. DNA aptamers, short DNA fragments that mimic antibody action, are currently being developed and considered as the future of antibody-like ligands. These molecules offer undeniable advantages: unparalleled ease of production, very high stability in air, similar affinity constants to antibodies, and compatibility with many organic solvents. The use of peptides specific to EVs is also an exciting biochemical solution to target EV membrane proteins and complement other probes. These different ligands have been used in several types of biosensors: electrochemical, optical, microfluidic using both generic probes (targeting widely expressed membrane proteins such as the tetraspanins) and specific probes (targeting disease biomarkers such as proteins overexpressed in cancer).
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Affiliation(s)
- M Gaillard
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France.
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Sato Y, Kuwahara K, Mogami K, Takahashi K, Nishizawa S. Amphipathic helical peptide-based fluorogenic probes for a marker-free analysis of exosomes based on membrane-curvature sensing. RSC Adv 2020; 10:38323-38327. [PMID: 35517518 PMCID: PMC9057301 DOI: 10.1039/d0ra07763a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/11/2020] [Indexed: 01/08/2023] Open
Abstract
With increasing knowledge about the diverse roles of exosomes in the biological process, much attention has been paid to develop analytical methods for detection and quantification of exosomes. Immunoassays based on the recognition of exosomal protein markers by antibodies were widely used. However, considering that exosomal protein composition varies with the cell type, the protein markers should be carefully selected for a sensitive and selective analysis of target exosomes. Herein, we developed a new class of exosome-binding fluorogenic probes based on membrane curvature (MC) sensing of amphipathic helical (AH) peptides for exosome analysis without the need to use protein markers on the exosomal membranes. The C-terminal region of apolipoprotein A-I labeled with Nile red (ApoC-NR) exhibited a significant fluorescence enhancement upon selective binding to the highly curved membranes of synthetic vesicles. Circular dichroism (CD) measurements involving 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/1-2-dioleoyl-sn-glycerol (DOG) vesicles suggested that ApoC-NR recognizes the lipid packing defects in the surface of highly curved membranes via the hydrophobic insertion of the α-helix structure of the ApoC unit. ApoC-NR exhibited a stronger binding affinity for exosome-sized vesicles and a higher MC selectivity compared to all other previously reported peptide probes. ApoC-NR can be used in a simple and rapid “mix and read” analysis of various kinds of exosomes derived from different cell types (limit of detection: –105 particles/μL) without being influenced by the variation in the expression of the surface proteins of the exosomes, which stands in sharp contrast to immunoassays. Fluorogenic probes based on membrane curvature sensing-amphipathic helical peptides have been developed for a marker-free exosome analysis.![]()
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kazuki Kuwahara
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kenta Mogami
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kenta Takahashi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Seiichi Nishizawa
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
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Abstract
This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.
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Affiliation(s)
- Ivan V Smolyar
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Valentine G Nenajdenko
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
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Affiliation(s)
- Teresa L. Mako
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Joan M. Racicot
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Mindy Levine
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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Liu Q, Jia Z, Duan L, Xiong J, Wang D, Ding Y. Functional peptides for cartilage repair and regeneration. Am J Transl Res 2018; 10:501-510. [PMID: 29511444 PMCID: PMC5835815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/10/2018] [Indexed: 06/08/2023]
Abstract
Cartilage repair after degeneration or trauma continues to be a challenge both in the clinic and for scientific research due to the limited regenerative capacity of this tissue. Cartilage tissue engineering, involving a combination of cells, scaffolds, and growth factors, is increasingly used in cartilage regeneration. Due to their ease of synthesis, robustness, tunable size, availability of functional groups, and activity, peptides have emerged as the molecules with the most potential in drug development. A number of peptides have been engineered to regenerate cartilage by acting as scaffolds, functional molecules, or both. In this paper, we will summarize the application of peptides in cartilage tissue engineering and discuss additional possibilities for peptides in this field.
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Affiliation(s)
- Qisong Liu
- Department of Orthopedic, Memorial Hospital of Sun Yat-sen UniversityGuangzhou 510120, Guangdong Province, China
- Shenzhen Key Laboratory of Tissue Engineering, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Department of Orthopedics, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic TechnologyShenzhen 518035, Guangdong Province, China
| | - Zhaofeng Jia
- Shenzhen Key Laboratory of Tissue Engineering, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Department of Orthopedics, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic TechnologyShenzhen 518035, Guangdong Province, China
| | - Li Duan
- Shenzhen Key Laboratory of Tissue Engineering, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Department of Orthopedics, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic TechnologyShenzhen 518035, Guangdong Province, China
| | - Jianyi Xiong
- Shenzhen Key Laboratory of Tissue Engineering, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Department of Orthopedics, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic TechnologyShenzhen 518035, Guangdong Province, China
| | - Daping Wang
- Shenzhen Key Laboratory of Tissue Engineering, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Department of Orthopedics, Shenzhen Second People’s HospitalShenzhen 518035, Guangdong Province, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic TechnologyShenzhen 518035, Guangdong Province, China
| | - Yue Ding
- Department of Orthopedic, Memorial Hospital of Sun Yat-sen UniversityGuangzhou 510120, Guangdong Province, China
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Kastelowitz N, Tamura R, Onasoga A, Stalker TJ, White OR, Brown PN, Brodsky GL, Brass LF, Branchford BR, Di Paola J, Yin H. Peptides derived from MARCKS block coagulation complex assembly on phosphatidylserine. Sci Rep 2017; 7:4275. [PMID: 28655899 PMCID: PMC5487340 DOI: 10.1038/s41598-017-04494-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/16/2017] [Indexed: 01/27/2023] Open
Abstract
Blood coagulation involves activation of platelets and coagulation factors. At the interface of these two processes resides the lipid phosphatidylserine. Activated platelets expose phosphatidylserine on their outer membrane leaflet and activated clotting factors assemble into enzymatically active complexes on the exposed lipid, ultimately leading to the formation of fibrin. Here, we describe how small peptide and peptidomimetic probes derived from the lipid binding domain of the protein myristoylated alanine-rich C-kinase substrate (MARCKS) bind to phosphatidylserine exposed on activated platelets and thereby inhibit fibrin formation. The MARCKS peptides antagonize the binding of factor Xa to phosphatidylserine and inhibit the enzymatic activity of prothrombinase. In whole blood under flow, the MARCKS peptides colocalize with, and inhibit fibrin cross-linking, of adherent platelets. In vivo, we find that the MARCKS peptides circulate to remote injuries and bind to activated platelets in the inner core of developing thrombi.
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Affiliation(s)
- Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Ryo Tamura
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Abimbola Onasoga
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Timothy J Stalker
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ormacinda R White
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Peter N Brown
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Gary L Brodsky
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Lawrence F Brass
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brian R Branchford
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jorge Di Paola
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA.
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA.
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de Jesus AJ, White OR, Flynn AD, Yin H. Determinants of Curvature-Sensing Behavior for MARCKS-Fragment Peptides. Biophys J 2017; 110:1980-92. [PMID: 27166806 DOI: 10.1016/j.bpj.2016.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/31/2016] [Accepted: 04/06/2016] [Indexed: 12/21/2022] Open
Abstract
It is increasingly recognized that membrane curvature plays an important role in various cellular activities such as signaling and trafficking, as well as key issues involving health and disease development. Thus, curvature-sensing peptides are essential to the study and detection of highly curved bilayer structures. The effector domain of myristoylated alanine-rich C-kinase substrate (MARCKS-ED) has been demonstrated to have curvature-sensing ability. Research of the MARCKS-ED has further revealed that its Lys and Phe residues play an essential role in how MARCKS-ED detects and binds to curved bilayers. MARCKS-ED has the added property of being a lower-molecular-weight curvature sensor, which offers advantages in production. With that in mind, this work investigates peptide-sequence-related factors that influence curvature sensing and explores whether peptide fragments of even shorter length can function as curvature sensors. Using both experimental and computational methods, we studied the curvature-sensing capabilities of seven fragments of MARCKS-ED. Two of the longer fragments were designed from approximately the two halves of the full-length peptide whereas the five shorter fragments were taken from the central stretch of MARCKS-ED. Fully atomistic molecular dynamics simulations show that the fragments that remain bound to the bilayer exhibit interactions with the bilayer similar to that of the full-length MARCKS-ED peptide. Fluorescence enhancement and anisotropy assays, meanwhile, reveal that five of the MARCKS fragments possess the ability to sense membrane curvature. Based on the sequences of the curvature-sensing fragments, it appears that the ability to sense curvature involves a balance between the numbers of positively charged residues and hydrophobic anchoring residues. Together, these findings help crystallize our understanding of the molecular mechanisms underpinning the curvature-sensing behaviors of peptides, which will prove useful in the design of future curvature sensors.
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Affiliation(s)
- Armando J de Jesus
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado; BioFrontiers Institute, University of Colorado, Boulder, Colorado
| | - Ormacinda R White
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado; BioFrontiers Institute, University of Colorado, Boulder, Colorado
| | - Aaron D Flynn
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado; BioFrontiers Institute, University of Colorado, Boulder, Colorado
| | - Hang Yin
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado; BioFrontiers Institute, University of Colorado, Boulder, Colorado.
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9
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Hosseini AS, Wang W, Haeffner F, Gao J. Metal-Assisted Folding of Prolinomycin Allows Facile Design of Functional Peptides. Chembiochem 2017; 18:479-482. [PMID: 28042934 DOI: 10.1002/cbic.201600667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 11/07/2022]
Abstract
Cyclic peptides have been proposed as privileged scaffolds that might mimic the folding and function of natural proteins. However, simple cyclic peptides typically cannot fold into well-defined structures. Herein, we describe a foldable cyclic peptide scaffold on which functional side chains can be displayed for targeted recognition of biomolecules. The foldable scaffold is based on prolinomycin, a proline-rich analogue of valinomycin. We report synthetic mutants of prolinomycin that retain the metal-assisted folding behavior under physiological conditions. The predictable structure formation of prolinomycin makes it a powerful platform to enable the development of synthetic receptors for biomolecules of interest. We demonstrate the potential of this scaffold by creating prolinomycin mutants that selectively bind anionic vesicles and bacterial cells.
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Affiliation(s)
- Azade S Hosseini
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
| | - Wenjian Wang
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
| | - Fredrik Haeffner
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
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10
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Shen C, Xue M, Qiu H, Guo W. Insertion of Neurotransmitters into a Lipid Bilayer Membrane and Its Implication on Membrane Stability: A Molecular Dynamics Study. Chemphyschem 2017; 18:626-633. [PMID: 28054433 DOI: 10.1002/cphc.201601184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/13/2016] [Indexed: 12/29/2022]
Abstract
The signaling molecules in neurons, called neurotransmitters, play an essential role in the transportation of neural signals, during which the neurotransmitters interact with not only specific receptors, but also cytomembranes, such as synaptic vesicle membranes and postsynaptic membranes. Through extensive molecular dynamics simulations, the atomic-scale insertion dynamics of typical neurotransmitters, including methionine enkephalin (ME), leucine enkephalin (LE), dopamine (DA), acetylcholine (ACh), and aspartic acid (ASP), into lipid bilayers is investigated. The results show that the first three neurotransmitters (ME, LE, and DA) are able to diffuse freely into both 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) membranes, and are guided by the aromatic residues Tyr and Phe. Only a limited number of these neurotransmitters are allowed to penetrate into the membrane, which suggests an intrinsic mechanism by which the membrane is protected from being destroyed by excessive inserted neurotransmitters. After spontaneous insertion, the neurotransmitters disturb the surrounding phospholipids in the membrane, as indicated by the altered distribution of components in lipid leaflets and the disordered lipid tails. In contrast, the last two neurotransmitters (ACh and ASP) cannot enter the membrane, but instead always diffuse freely in solution. These findings provide an understanding at the atomic level of how neurotransmitters interact with the surrounding cytomembrane, as well as their impact on membrane behavior.
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Affiliation(s)
- Chun Shen
- State Key Laboratory of Mechanics and Control of Mechanical Structure and Key Laboratory for Intelligent Nano Materials and Devices of the, Ministry of Education, and Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, P.R. China
| | - Minmin Xue
- State Key Laboratory of Mechanics and Control of Mechanical Structure and Key Laboratory for Intelligent Nano Materials and Devices of the, Ministry of Education, and Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, P.R. China
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structure and Key Laboratory for Intelligent Nano Materials and Devices of the, Ministry of Education, and Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, P.R. China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structure and Key Laboratory for Intelligent Nano Materials and Devices of the, Ministry of Education, and Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, P.R. China
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11
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Abstract
Extracellular vesicles (EVs) are submicroscopic lipid vesicles secreted from cells and play significant roles in cell-to-cell communication by transporting varieties of cell signaling molecules like proteins, DNA, mRNA, and microRNA. Recent studies showed that EVs are highly correlated with cancer progression and metastasis. However, there are some difficulties in probing each vesicle using popular analytical methods because of their small sizes and heterogeneous origins. These obstacles may be overcome by using a novel approach that senses highly curved membrane and negatively charged membrane lipids. In this chapter, we highlight the basic biological concepts of EVs, isolation, and quantification methods, and recent advent of peptide probes for EVs.
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Affiliation(s)
- R Tamura
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States
| | - H Yin
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States.
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12
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Abstract
Computer simulations have become an indispensable tool in studying molecular biological systems. The unmatched spatial and temporal resolution that it offers enables for microscopic-level views into the dynamics and mechanics of biological systems. Recent advances in hardware resources have also opened up to computer simulations the investigation of longer timescale biological processes and larger systems. The study of membrane proteins or peptides especially benefits from simulations due to difficulties related to crystallization of such proteins in a membrane environment. In this chapter, we outline the method of molecular dynamics and how it is applied to simulations that involve a peptide and lipid bilayers. In particular, the simulation of a membrane-curvature sensing peptide is examined, and ways of employing computational simulations to design such peptides are discussed.
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Affiliation(s)
- Armando Jerome de Jesus
- Department of Chemistry and Biochemistry and The BioFrontiers Institute, University of Colorado, UCB 596, Boulder, CO, 80309, USA
| | - Hang Yin
- Department of Chemistry and Biochemistry and The BioFrontiers Institute, University of Colorado, UCB 596, Boulder, CO, 80309, USA.
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13
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Gao M, Cheng K, Yin H. Targeting protein-protein interfaces using macrocyclic peptides. Biopolymers 2016; 104:310-6. [PMID: 25664609 DOI: 10.1002/bip.22625] [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: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 01/10/2023]
Abstract
Protein-protein interactions (PPIs) are critical in numerous biological processes including signaling transduction, function regulations, and disease development. To regulate PPIs has been thought to be challenging due to their highly dynamic and expansive interfacial areas. Nonetheless, successful examples have been reported of targeting PPIs using small molecules, peptides, and proteins. Peptides, especially macrocyclic peptides have proven to be a particularly useful tool to inhibit PPIs for their exquisite potency, stability and selectivity. Herein we review the recent developments of this area of research, focusing on the macrocyclic peptides isolated from natural products, identified from library screening, and rationally designed based on structures, as PPI regulators.
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Affiliation(s)
- Meng Gao
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Kui Cheng
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Hang Yin
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082.,Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309-0596
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14
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Gilliam AJH, Smith JN, Flather D, Johnston KM, Gansmiller AM, Fishman DA, Edgar JM, Balk M, Majumdar S, Weiss GA. Affinity-Guided Design of Caveolin-1 Ligands for Deoligomerization. J Med Chem 2016; 59:4019-25. [PMID: 27010220 DOI: 10.1021/acs.jmedchem.5b01536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Caveolin-1 is a target for academic and pharmaceutical research due to its many cellular roles and associated diseases. We report peptide WL47 (1), a small, high-affinity, selective disrupter of caveolin-1 oligomers. Developed and optimized through screening and analysis of synthetic peptide libraries, ligand 1 has 7500-fold improved affinity compared to its T20 parent ligand and an 80% decrease in sequence length. Ligand 1 will permit targeted study of caveolin-1 function.
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Affiliation(s)
- Amanda J H Gilliam
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Joshua N Smith
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Dylan Flather
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Kevin M Johnston
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Andrew M Gansmiller
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Dmitry A Fishman
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Joshua M Edgar
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Mark Balk
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Sudipta Majumdar
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
| | - Gregory A Weiss
- Department of Chemistry, and ‡Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697-2025, United States
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15
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Saludes JP, Gregar TQ, Monreal IA, Cook BM, Danan-Leon LM, Gervay-Hague J. Solution phase conformation and proteolytic stability of amide-linked neuraminic acid analogues. Biopolymers 2016; 99:686-96. [PMID: 23765412 DOI: 10.1002/bip.22315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/31/2013] [Indexed: 11/10/2022]
Abstract
Amide-linked homopolymers of sialic acid offer the advantages of stable secondary structure and increased bioavailability making them useful constructs for pharmaceutical design and drug delivery. Defining the structural characteristics that give rise to secondary structure in aqueous solution is challenging in homopolymeric material due to spectral overlap in NMR spectra. Having previously developed computational tools for heteroologomers with resolved spectra, we now report that application of these methods in combination with circular dichroism, NH/ND NMR exchange rates and nOe data has enabled the structural determination of a neutral, δ-amide-linked homopolymer of a sialic acid analogue called Neu2en. The results show that the inherent planarity of the pyranose ring in Neu2en brought about by the α,δ-conjugated amide bond serves as the primary driving force of the overall conformation of the homooligomer. This peptide surrogate has an excellent bioavailability profile, with half-life of ∼12 h in human blood serum, which offers a viable peptide scaffold that is resistant to proteolytic degradation. Furthermore, a proof-of-principle study illustrates that Neu2en oligomers are functionalizable with small molecule ligands using 1,3-dipolar cycloaddition chemistry.
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Affiliation(s)
- Jonel P Saludes
- Department of Chemistry, , University of California Davis, One Shields Ave., Davis, CA, 95616; Department of Chemistry, Washington State University, Pullman, WA, 99164
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16
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Yan L, Liang J, Yin H. Chemical Biology Probes for Extracellular Vesicles Facilitate Studies of Neuroinflammation. ACS Chem Neurosci 2016; 7:418-9. [PMID: 26654245 DOI: 10.1021/acschemneuro.5b00310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Neuroinflammation has been conceived as an important cause for or contributor to neurological diseases. With major strides in new technology, scientists can use chemical biology tools developed in non-neuronal systems to research neuroinflammation. Extracellular vesicles (EVs) play a vital role in mediating neuroinflammation via carrying pathogenic misfolded proteins as well as nucleic acids, suggesting important biological functions. Nonetheless, it is a daunting goal to study these ultramicroscopic EVs in part due to the technical hurdle of specific labeling and preparation. Therefore, development of new detection methods of EVs will promote further understanding of EVs in the nervous system, thereby expediting the diagnosis and therapy development for neurological disorders. Recent progress toward a new class of chemical biology probes simultaneously targeting the highly curved surface and the particular lipid compositions of EVs may offer an alternative strategy for their detection, isolation, and purification, which not only will facilitate research on their mechanism in neuroinflammation and neurological diseases, but also may lay the groundwork for the next generation of diagnostics and prognostics.
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Affiliation(s)
- Lei Yan
- Center of Basic
Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Jiaqi Liang
- Center of Basic
Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Hang Yin
- Center of Basic
Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
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17
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Abstract
The majority of therapeutics target membrane proteins, accessible on the surface of cells, to alter cellular signaling. Cells use membrane proteins to transduce signals into cells, transport ions and molecules, bind cells to a surface or substrate, and catalyze reactions. Newly devised technologies allow us to drug conventionally "undruggable" regions of membrane proteins, enabling modulation of protein-protein, protein-lipid, and protein-nucleic acid interactions. In this review, we survey the state of the art of high-throughput screening and rational design in drug discovery, and we evaluate the advances in biological understanding and technological capacity that will drive pharmacotherapy forward against unorthodox membrane protein targets.
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Affiliation(s)
- Hang Yin
- Department of Chemistry and Biochemistry.,BioFrontiers Institute, and.,Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Aaron D Flynn
- BioFrontiers Institute, and.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309; ,
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18
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Castro V, Rodríguez H, Albericio F. CuAAC: An Efficient Click Chemistry Reaction on Solid Phase. ACS COMBINATORIAL SCIENCE 2016; 18:1-14. [PMID: 26652044 DOI: 10.1021/acscombsci.5b00087] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Click chemistry is an approach that uses efficient and reliable reactions, such as Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), to bind two molecular building blocks. CuAAC has broad applications in medicinal chemistry and other fields of chemistry. This review describes the general features and applications of CuAAC in solid-phase synthesis (CuAAC-SP), highlighting the suitability of this kind of reaction for peptides, nucleotides, small molecules, supramolecular structures, and polymers, among others. This versatile reaction is expected to become pivotal for meeting future challenges in solid-phase chemistry.
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Affiliation(s)
- Vida Castro
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
| | - Hortensia Rodríguez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
- School
of Chemistry, Yachay Tech, Yachay City of Knowledge, Urcuqui, Ecuador
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona, 08028-Barcelona, Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001-Durban, South Africa
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19
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Zhang L, Yethiraj A, Cui Q. Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models. J Chem Theory Comput 2015; 10:2845-59. [PMID: 26586509 DOI: 10.1021/ct500218p] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The binding of peptides and proteins to the surface of complex lipid membranes is important in many biological processes such as cell signaling and membrane remodeling. Computational studies can aid experiments by identifying physical interactions and structural motifs that determine the binding affinity and specificity. However, previous studies focused on either qualitative behaviors of protein/membrane interactions or the binding affinity of small peptides. Motivated by this observation, we set out to develop computational protocols for bimolecular binding to charged membranes that are applicable to both peptides and large proteins. In this work, we explore a method based on an implicit membrane/solvent model (generalized Born with a simple switching in combination with the Gouy-Chapman-Stern model for a charged interface), which we expect to lead to useful results when the binding does not implicate significant membrane deformation and local demixing of lipids. We show that the binding free energy can be efficiently computed following a thermodynamic cycle similar to protein-ligand binding calculations, especially when a Bennett acceptance ratio based protocol is used to consider both the membrane bound and solution conformational ensembles. Test calculations on a series of peptides show that our computational approach leads to binding affinities in encouraging agreement with experimental data, including for the challenging example of the bringing of flexible MARCKS-ED peptides to membranes. The calculations highlight that for a membrane with a significant fraction of anionic lipids, it is essential to include the effect of ion adsorption using the Stern model, which significantly modifies the effective surface charge. This implicit membrane model based computational protocol helps lay the groundwork for more systematic analysis of protein/peptide binding to membranes of complex shape and composition.
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Affiliation(s)
- Leili Zhang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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20
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Wu Z, Schulten K. Synaptotagmin's role in neurotransmitter release likely involves Ca(2+)-induced conformational transition. Biophys J 2015; 107:1156-66. [PMID: 25185551 DOI: 10.1016/j.bpj.2014.07.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/15/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022] Open
Abstract
Neuronal exocytosis is mediated by a Ca(2+)-triggered membrane fusion event that joins synaptic vesicles and presynaptic membrane. In this event, synaptotagmin I plays a key role as a Ca(2+) sensor protein that binds to and bends the presynaptic membrane with its C2B domain, and thereby initiates membrane fusion. We report free energy calculations according to which C2B-induced membrane bending is preceded by a Ca(2+)- and membrane-dependent conformational transition. In this transition C2B attaches to the membrane, moves its C-terminal helix from the orientation seen in the available (but membrane-free) crystal/NMR structures as pointing away from the membrane (helix-up), to an orientation pointing toward the membrane (helix-down). In the C2B helix-down state, lipid tails in the proximal membrane bilayer leaflet interact with the moved helix and become disordered, whereas tails in the distal leaflet, to keep in contact with the proximal leaflet, become stretched and ordered. The difference in lipid tail packing between the two leaflets results in an imbalance of pressure across the membrane, and thereby causes membrane bending. The lipid-disordering monitored in the simulations is well suited to facilitate Ca(2+)-triggered membrane fusion.
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Affiliation(s)
- Zhe Wu
- Department of Physics, Center for the Physics of Living Cells, Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois
| | - Klaus Schulten
- Department of Physics, Center for the Physics of Living Cells, Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois.
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21
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Yan L, de Jesus AJ, Tamura R, Li V, Cheng K, Yin H. Curvature sensing MARCKS-ED peptides bind to membranes in a stereo-independent manner. J Pept Sci 2015; 21:577-585. [PMID: 25851418 DOI: 10.1002/psc.2772] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/16/2015] [Accepted: 02/18/2015] [Indexed: 12/21/2022]
Abstract
Membrane curvature and lipid composition plays a critical role in interchanging of matter and energy in cells. Peptide curvature sensors are known to activate signaling pathways and promote molecular transport across cell membranes. Recently, the 25-mer MARCKS-ED peptide, which is derived from the effector domain of the myristoylated alanine-rich C kinase substrate protein, has been reported to selectively recognize highly curved membrane surfaces. Our previous studies indicated that the naturally occurring L-MARCKS-ED peptide could simultaneously detect both phosphatidylserine and curvature. Here, we demonstrate that D-MARCKS-ED, composed by unnatural D-amino acids, has the same activities as its enantiomer, L-MARCKS-ED, as a curvature and lipid sensor. An atomistic molecular dynamics simulation suggests that D-MARCKS-ED may change from linear to a boat conformation upon binding to the membrane. Comparable enhancement of fluorescence intensity was observed between D- and L-MARCKS-ED peptides, indicating similar binding affinities. Meanwhile, circular dichroism spectra of D- and L-MARCKS-ED are almost symmetrical both in the presence and absence of liposomes. These results suggest similar behavior of artificial D- and natural L-MARCKS-ED peptides when binding to curved membranes. Our studies may contribute to further understanding of how MARCKS-ED senses membrane curvature as well as provide a new direction to develop novel membrane curvature probes.
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Affiliation(s)
- Lei Yan
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China, 100082
| | - Armando Jerome de Jesus
- Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309-0596, USA
| | - Ryo Tamura
- Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309-0596, USA
| | - Victoria Li
- Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309-0596, USA
| | - Kui Cheng
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China, 100082
| | - Hang Yin
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China, 100082.,Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309-0596, USA
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22
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Gunasekara RW, Zhao Y. Conformationally switchable water-soluble fluorescent bischolate foldamers as membrane-curvature sensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3919-3925. [PMID: 25782344 DOI: 10.1021/acs.langmuir.5b00379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Membrane curvature is an important parameter in biological processes such as cellular movement, division, and vesicle fusion and budding. Traditionally, only proteins and protein-derived peptides have been used as sensors for membrane curvature. Three water-soluble bischolate foldamers were synthesized, all labeled with an environmentally sensitive fluorophore to report their binding with lipid membranes. The orientation and ionic nature of the fluorescent label were found to be particularly important in their performance as membrane-curvature sensors. The bischolate with an NBD group in the hydrophilic α-face of the cholate outperformed the other two analogues as a membrane-curvature sensor and responded additionally to the lipid composition including the amounts of cholesterol and anionic lipids in the membranes.
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Affiliation(s)
- Roshan W Gunasekara
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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23
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Kastelowitz N, Yin H. Exosomes and microvesicles: identification and targeting by particle size and lipid chemical probes. Chembiochem 2014; 15:923-8. [PMID: 24740901 PMCID: PMC4098878 DOI: 10.1002/cbic.201400043] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Indexed: 12/21/2022]
Abstract
Exosomes and microvesicles are two classes of submicroscopic vesicle released by cells into the extracellular space. Collectively referred to as extracellular vesicles, these membrane containers facilitate important cell-cell communication by carrying a diverse array of signaling molecules, including nucleic acids, proteins, and lipids. Recently, the role of extracellular vesicle signaling in cancer progression has become a topic of significant interest. Methods to detect and target exosomes and microvesicles are needed to realize applications of extracellular vesicles as biomarkers and, perhaps, therapeutic targets. Detection of exosomes and microvesicles is a complex problem as they are both submicroscopic and of heterogeneous cellular origins. In this Minireview, we highlight the basic biology of extracellular vesicles, and address available biochemical and biophysical detection methods. Detectible characteristics described here include lipid and protein composition, and physical properties such as the vesicle membrane shape and diffusion coefficient. In particular, we propose that detection of exosome and microvesicle membrane curvature with lipid chemical probes that sense membrane shape is a distinctly promising method for identifying and targeting these vesicles.
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Affiliation(s)
- Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute,
University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80303 (USA)
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute,
University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80303 (USA)
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24
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Illuminating the lipidome to advance biomedical research: peptide-based probes of membrane lipids. Future Med Chem 2013; 5:947-59. [PMID: 23682570 DOI: 10.4155/fmc.13.66] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Systematic investigation of the lipidome will reveal new opportunities for disease diagnosis and intervention. However, lipidomic research has been hampered by the lack of molecular tools to track specific lipids of interest. Accumulating reports indicate lipid recognition can be achieved with properly constructed short peptides in addition to large proteins. This review summarizes the key developments of this area within the past decade. Select lantibiotic peptides present the best examples of low-molecular-weight probes of membrane lipids, displaying selectivity comparable to lipid-binding proteins. Designed peptides, through biomimetic approaches and combinational screening, have begun to demonstrate their potential for lipid tracking in cultured cells and even in living organisms. Biophysical characterization of these lipid-targeting peptides has revealed certain features critical for selective membrane binding, including preorganized scaffolds and the balance of polar and nonpolar interactions. The knowledge summarized herein should facilitate the development of molecular tools to target a variety of membrane lipids.
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25
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Pasini D. The click reaction as an efficient tool for the construction of macrocyclic structures. Molecules 2013; 18:9512-30. [PMID: 23966075 PMCID: PMC6270095 DOI: 10.3390/molecules18089512] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 12/24/2022] Open
Abstract
The Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC, known as the click reaction) is an established tool used for the construction of complex molecular architectures. Given its efficiency it has been widely applied for bioconjugation, polymer and dendrimer synthesis. More recently, this reaction has been utilized for the efficient formation of rigid or shape-persistent, preorganized macrocyclic species. This strategy also allows the installment of useful functionalities, in the form of polar and function-rich 1,2,3-triazole moieties, directly embedded in the macrocyclic structures. This review analyzes the state of the art in this context, and provides some elements of perspective for future applications.
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Affiliation(s)
- Dario Pasini
- Department of Chemistry, University of Pavia, Viale Taramelli, 10-27100 Pavia, Italy.
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Saludes JP, Morton LA, Coulup SK, Fiorini Z, Cook BM, Beninson L, Chapman ER, Fleshner M, Yin H. Multivalency amplifies the selection and affinity of bradykinin-derived peptides for lipid nanovesicles. MOLECULAR BIOSYSTEMS 2013; 9:2005-9. [PMID: 23715428 PMCID: PMC3764994 DOI: 10.1039/c3mb70109c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The trimer of a bradykinin derivative displayed a more than five-fold increase in binding affinity for phosphatidylserine-enriched nanovesicles as compared to its monomeric precursor. The nanovesicle selection is directly correlated with multivalency, which amplifies the electrostatic attraction. This strategy may lead to the development of novel molecular probes for detecting highly curved membrane bilayers.
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Affiliation(s)
- Jonel P. Saludes
- Department of Chemistry & Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Leslie A. Morton
- Department of Chemistry & Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Sara K. Coulup
- Department of Chemistry & Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Zeno Fiorini
- Department of Chemistry & Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Brandan M. Cook
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Lida Beninson
- Department of Integrative Physiology, University of Colorado, Boulder, CO 80309, USA
| | - Edwin R. Chapman
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin, Madison, WI 53706, USA
| | - Monika Fleshner
- Department of Integrative Physiology, University of Colorado, Boulder, CO 80309, USA
| | - Hang Yin
- Department of Chemistry & Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
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Sokolova NV, Nenajdenko VG. Recent advances in the Cu(i)-catalyzed azide–alkyne cycloaddition: focus on functionally substituted azides and alkynes. RSC Adv 2013. [DOI: 10.1039/c3ra42482k] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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