1
|
Ruixuan H, Majee A, Dobnikar J, Podgornik R. Electrostatic interactions between charge regulated spherical macroions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:115. [PMID: 38019363 DOI: 10.1140/epje/s10189-023-00373-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023]
Abstract
We study the interaction between two charge regulating spherical macroions with dielectric interior and dissociable surface groups immersed in a monovalent electrolyte solution. The charge dissociation is modelled via the Frumkin-Fowler-Guggenheim isotherm, which allows for multiple adsorption equilibrium states. The interactions are derived from the solutions of the mean-field Poisson-Boltzmann type theory with charge regulation boundary conditions. For a range of conditions we find symmetry breaking transitions from symmetric to asymmetric charge distribution exhibiting annealed charge patchiness, which results in like-charge attraction even in a univalent electrolyte-thus fundamentally modifying the nature of electrostatic interactions in charge-stabilized colloidal suspensions.
Collapse
Affiliation(s)
- Hu Ruixuan
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Arghya Majee
- Max Planck Institute for the Physics of Complex Systems, 01187, Dresden, Germany
| | - Jure Dobnikar
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- Songshan Lake Materials Laboratory, Guangdong, 523808, Dongguan, China
| | - Rudolf Podgornik
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China.
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000, Ljubljana, Slovenia.
| |
Collapse
|
2
|
Vahid H, Scacchi A, Sammalkorpi M, Ala-Nissila T. Interactions between Rigid Polyelectrolytes Mediated by Ordering and Orientation of Multivalent Nonspherical Ions in Salt Solutions. PHYSICAL REVIEW LETTERS 2023; 130:158202. [PMID: 37115871 DOI: 10.1103/physrevlett.130.158202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/23/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Multivalent ions in solutions with polyelectrolytes (PEs) induce electrostatic correlations that can drastically change ion distributions around the PEs and their mutual interactions. Using coarse-grained molecular dynamics simulations, we show how in addition to valency, ion shape and concentration can be harnessed as tools to control rigid like-charged PE-PE interactions. We demonstrate a correlation between the orientational ordering of aspherical ions and how they mediate the effective PE-PE attraction induced by multivalency. The interaction type, strength, and range can thus be externally controlled in ionic solutions. Our results can be used as generic guidelines to tune the self-assembly of like-charged polyelectrolytes by variation of the characteristics of the ions.
Collapse
Affiliation(s)
- Hossein Vahid
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
| |
Collapse
|
3
|
Nicastro LK, de Anda J, Jain N, Grando KCM, Miller AL, Bessho S, Gallucci S, Wong GCL, Tükel Ç. Assembly of ordered DNA-curli fibril complexes during Salmonella biofilm formation correlates with strengths of the type I interferon and autoimmune responses. PLoS Pathog 2022; 18:e1010742. [PMID: 35972973 PMCID: PMC9380926 DOI: 10.1371/journal.ppat.1010742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Deposition of human amyloids is associated with complex human diseases such as Alzheimer's and Parkinson's. Amyloid proteins are also produced by bacteria. The bacterial amyloid curli, found in the extracellular matrix of both commensal and pathogenic enteric bacterial biofilms, forms complexes with extracellular DNA, and recognition of these complexes by the host immune system may initiate an autoimmune response. Here, we isolated early intermediate, intermediate, and mature curli fibrils that form throughout the biofilm development and investigated the structural and pathogenic properties of each. Early intermediate aggregates were smaller than intermediate and mature curli fibrils, and circular dichroism, tryptophan, and thioflavin T analyses confirmed the establishment of a beta-sheet secondary structure as the curli conformations matured. Intermediate and mature curli fibrils were more immune stimulatory than early intermediate fibrils in vitro. The intermediate curli was cytotoxic to macrophages independent of Toll-like receptor 2. Mature curli fibrils had the highest DNA content and induced the highest levels of Isg15 expression and TNFα production in macrophages. In mice, mature curli fibrils induced the highest levels of anti-double-stranded DNA autoantibodies. The levels of autoantibodies were higher in autoimmune-prone NZBWxF/1 mice than wild-type C57BL/6 mice. Chronic exposure to all curli forms led to significant histopathological changes and synovial proliferation in the joints of autoimmune-prone mice; mature curli was the most detrimental. In conclusion, curli fibrils, generated during biofilm formation, cause pathogenic autoimmune responses that are stronger when curli complexes contain higher levels of DNA and in mice predisposed to autoimmunity.
Collapse
Affiliation(s)
- Lauren K. Nicastro
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jaime de Anda
- Department of Bioengineering, California Nano Systems Institute, University of California, Los Angeles, California, United States of America
| | - Neha Jain
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, India
| | - Kaitlyn C. M. Grando
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Amanda L. Miller
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Shingo Bessho
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Stefania Gallucci
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Gerard C. L. Wong
- Department of Bioengineering, California Nano Systems Institute, University of California, Los Angeles, California, United States of America
| | - Çagla Tükel
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
4
|
Xian W, Hennefarth MR, Lee MW, Do T, Lee EY, Alexandrova AN, Wong GCL. Histidine-Mediated Ion Specific Effects Enable Salt Tolerance of a Pore-Forming Marine Antimicrobial Peptide. Angew Chem Int Ed Engl 2022; 61:e202108501. [PMID: 35352449 DOI: 10.1002/anie.202108501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Indexed: 12/19/2022]
Abstract
Antimicrobial peptides (AMPs) preferentially permeate prokaryotic membranes via electrostatic binding and membrane remodeling. Such action is drastically suppressed by high salt due to increased electrostatic screening, thus it is puzzling how marine AMPs can possibly work. We examine as a model system, piscidin-1, a histidine-rich marine AMP, and show that ion-histidine interactions play unanticipated roles in membrane remodeling at high salt: Histidines can simultaneously hydrogen-bond to a phosphate and coordinate with an alkali metal ion to neutralize phosphate charge, thereby facilitating multidentate bonds to lipid headgroups in order to generate saddle-splay curvature, a prerequisite to pore formation. A comparison among Na+ , K+ , and Cs+ indicates that histidine-mediated salt tolerance is ion specific. We conclude that histidine plays a unique role in enabling protein/peptide-membrane interactions that occur in marine or other high-salt environment.
Collapse
Affiliation(s)
- Wujing Xian
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew R Hennefarth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michelle W Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tran Do
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.,California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.,California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
5
|
Grando K, Nicastro LK, Tursi SA, De Anda J, Lee EY, Wong GCL, Tükel Ç. Phenol-Soluble Modulins From Staphylococcus aureus Biofilms Form Complexes With DNA to Drive Autoimmunity. Front Cell Infect Microbiol 2022; 12:884065. [PMID: 35646719 PMCID: PMC9131096 DOI: 10.3389/fcimb.2022.884065] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/04/2022] [Indexed: 12/15/2022] Open
Abstract
The bacterial amyloid curli, produced by Enterobacteriales including Salmonella species and Escherichia coli, is implicated in the pathogenesis of several complex autoimmune diseases. Curli binds to extracellular DNA, and these complexes drive autoimmunity via production of anti-double-stranded DNA autoantibodies. Here, we investigated immune activation by phenol-soluble modulins (PSMs), the amyloid proteins expressed by Staphylococcus species. We confirmed the amyloid nature of PSMs expressed by S. aureus using a novel specific amyloid stain, (E,E)-1-fluoro-2,5-bis(3-hydroxycarbonyl-4-hydroxy) styrylbenzene (FSB). Direct interaction of one of the S. aureus PSMs, PSMα3, with oligonucleotides promotes fibrillization of PSM amyloids and complex formation with bacterial DNA. Finally, utilizing a mouse model with an implanted mesh-associated S. aureus biofilm, we demonstrated that exposure to S. aureus biofilms for six weeks caused anti-double-stranded DNA autoantibody production in a PSM-dependent manner. Taken together, these results highlight how the presence of PSM-DNA complexes in S. aureus biofilms can induce autoimmune responses, and suggest an explanation for how bacterial infections trigger autoimmunity.
Collapse
Affiliation(s)
- Kaitlyn Grando
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Lauren K. Nicastro
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Sarah A. Tursi
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Jaime De Anda
- Department of Bioengineering, Department of Chemistry and Biochemistry, California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ernest Y. Lee
- Department of Bioengineering, Department of Chemistry and Biochemistry, California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gerard C. L. Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Çağla Tükel
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
- *Correspondence: Çağla Tükel,
| |
Collapse
|
6
|
Xian W, Hennefarth MR, Lee MW, Do T, Lee EY, Alexandrova AN, Wong GCL. Histidine‐Mediated Ion Specific Effects Enable Salt Tolerance of a Pore‐Forming Marine Antimicrobial Peptide. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202108501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wujing Xian
- Department of Bioengineering University of California, Los Angeles Los Angeles CA 90095 USA
| | - Matthew R. Hennefarth
- Department of Chemistry and Biochemistry University of California, Los Angeles Los Angeles CA 90095 USA
| | - Michelle W. Lee
- Department of Bioengineering University of California, Los Angeles Los Angeles CA 90095 USA
| | - Tran Do
- Department of Bioengineering University of California, Los Angeles Los Angeles CA 90095 USA
| | - Ernest Y. Lee
- Department of Bioengineering University of California, Los Angeles Los Angeles CA 90095 USA
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry University of California, Los Angeles Los Angeles CA 90095 USA
- California Nano Systems Institute University of California, Los Angeles Los Angeles CA 90095 USA
| | - Gerard C. L. Wong
- Department of Bioengineering University of California, Los Angeles Los Angeles CA 90095 USA
- California Nano Systems Institute University of California, Los Angeles Los Angeles CA 90095 USA
| |
Collapse
|
7
|
Synthesis of multilamellar walls vesicles polyelectrolyte-surfactant complexes from pH-stimulated phase transition using microbial biosurfactants. J Colloid Interface Sci 2020; 580:493-502. [DOI: 10.1016/j.jcis.2020.07.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 11/20/2022]
|
8
|
Lee EY, Srinivasan Y, de Anda J, Nicastro LK, Tükel Ç, Wong GCL. Functional Reciprocity of Amyloids and Antimicrobial Peptides: Rethinking the Role of Supramolecular Assembly in Host Defense, Immune Activation, and Inflammation. Front Immunol 2020; 11:1629. [PMID: 32849553 PMCID: PMC7412598 DOI: 10.3389/fimmu.2020.01629] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Pathological self-assembly is a concept that is classically associated with amyloids, such as amyloid-β (Aβ) in Alzheimer's disease and α-synuclein in Parkinson's disease. In prokaryotic organisms, amyloids are assembled extracellularly in a similar fashion to human amyloids. Pathogenicity of amyloids is attributed to their ability to transform into several distinct structural states that reflect their downstream biological consequences. While the oligomeric forms of amyloids are thought to be responsible for their cytotoxicity via membrane permeation, their fibrillar conformations are known to interact with the innate immune system to induce inflammation. Furthermore, both eukaryotic and prokaryotic amyloids can self-assemble into molecular chaperones to bind nucleic acids, enabling amplification of Toll-like receptor (TLR) signaling. Recent work has shown that antimicrobial peptides (AMPs) follow a strikingly similar paradigm. Previously, AMPs were thought of as peptides with the primary function of permeating microbial membranes. Consistent with this, many AMPs are facially amphiphilic and can facilitate membrane remodeling processes such as pore formation and fusion. We show that various AMPs and chemokines can also chaperone and organize immune ligands into amyloid-like ordered supramolecular structures that are geometrically optimized for binding to TLRs, thereby amplifying immune signaling. The ability of amphiphilic AMPs to self-assemble cooperatively into superhelical protofibrils that form structural scaffolds for the ordered presentation of immune ligands like DNA and dsRNA is central to inflammation. It is interesting to explore the notion that the assembly of AMP protofibrils may be analogous to that of amyloid aggregates. Coming full circle, recent work has suggested that Aβ and other amyloids also have AMP-like antimicrobial functions. The emerging perspective is one in which assembly affords a more finely calibrated system of recognition and response: the detection of single immune ligands, immune ligands bound to AMPs, and immune ligands spatially organized to varying degrees by AMPs, result in different immunologic outcomes. In this framework, not all ordered structures generated during multi-stepped AMP (or amyloid) assembly are pathological in origin. Supramolecular structures formed during this process serve as signatures to the innate immune system to orchestrate immune amplification in a proportional, situation-dependent manner.
Collapse
Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yashes Srinivasan
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lauren K Nicastro
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Çagla Tükel
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States.,California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
9
|
Lee EY, Takahashi T, Curk T, Dobnikar J, Gallo RL, Wong GCL. Crystallinity of Double-Stranded RNA-Antimicrobial Peptide Complexes Modulates Toll-Like Receptor 3-Mediated Inflammation. ACS NANO 2017; 11:12145-12155. [PMID: 29016111 PMCID: PMC5936640 DOI: 10.1021/acsnano.7b05234] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Double-stranded RNA (dsRNA) induces production of pro-inflammatory cytokines in normal human epidermal keratinocytes (NHEK) by specific binding to endosomal Toll-like receptor-3 (TLR3). Recently, it has been shown that hyperactivation of TLR3 in psoriatic keratinocytes by dsRNA can occur in the presence of human antimicrobial peptide (AMP) LL37. Here, we combine synchrotron X-ray scattering, microscopy, computer simulations, and measurements of NHEK cytokine production to elucidate a previously unanticipated form of specific molecular pattern recognition. LL37 and similar α-helical AMPs can form pro-inflammatory nanocrystalline complexes with dsRNA that are recognized by TLR3 differently than dsRNA alone. dsRNA complexes that activate IL-6 production in NHEK and those that do not are both able to enter cells and co-localize with TLR3. However, the crystallinity of these AMP-dsRNA complexes, specifically the geometric spacing between parallel dsRNA and the repeat number of ordered dsRNA, strongly influences the level of TLR3 activation. Crystalline complexes that present dsRNA at a spacing that matches with the steric size of TLR3 can recruit and engage multiple TLR3 receptors, driving receptor clustering and immune amplification, whereas crystalline complexes that exhibit poor steric matching do not. Reverse-transcription quantitative PCR of IL-6 during siRNA knockdown of TLR3 confirms that cytokine production is due to TLR3: High levels of IL-6 transcription are observed for sterically matched complexes without TLR3 knockdown, whereas such activity is abrogated with TLR3 knockdown.
Collapse
Affiliation(s)
- Ernest Y. Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Toshiya Takahashi
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093, United States
| | - Tine Curk
- Beijing National Laboratory for Condensed Matter Physics & CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jure Dobnikar
- Beijing National Laboratory for Condensed Matter Physics & CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Department of Chemistry, University of Cambridge, Cambridge, UK
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- To whom correspondence should be addressed: Gerard C.L. Wong, Department of Bioengineering, University of California, Los Angeles, 4121 Engineering V UCLA Los Angeles, CA 90095. Tel: (310) 794-7684 , Richard L. Gallo, Department of Dermatology, University of California, San Diego, 3350 La Jolla Village Drive, San Diego, CA 92161. , Jure Dobnikar, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
| | - Richard L. Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093, United States
- To whom correspondence should be addressed: Gerard C.L. Wong, Department of Bioengineering, University of California, Los Angeles, 4121 Engineering V UCLA Los Angeles, CA 90095. Tel: (310) 794-7684 , Richard L. Gallo, Department of Dermatology, University of California, San Diego, 3350 La Jolla Village Drive, San Diego, CA 92161. , Jure Dobnikar, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
| | - Gerard C. L. Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
- To whom correspondence should be addressed: Gerard C.L. Wong, Department of Bioengineering, University of California, Los Angeles, 4121 Engineering V UCLA Los Angeles, CA 90095. Tel: (310) 794-7684 , Richard L. Gallo, Department of Dermatology, University of California, San Diego, 3350 La Jolla Village Drive, San Diego, CA 92161. , Jure Dobnikar, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
10
|
Safinya CR, Chung PJ, Song C, Li Y, Ewert KK, Choi MC. The effect of multivalent cations and Tau on paclitaxel-stabilized microtubule assembly, disassembly, and structure. Adv Colloid Interface Sci 2016; 232:9-16. [PMID: 26684364 PMCID: PMC4864139 DOI: 10.1016/j.cis.2015.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/29/2015] [Accepted: 11/04/2015] [Indexed: 01/22/2023]
Abstract
In this review we describe recent studies directed at understanding the formation of novel nanoscale assemblies in biological materials systems. In particular, we focus on the effects of multivalent cations, and separately, of microtubule-associated protein (MAP) Tau, on microtubule (MT) ordering (bundling), MT disassembly, and MT structure. Counter-ion directed bundling of paclitaxel-stabilized MTs is a model electrostatic system, which parallels efforts to understand MT bundling by intrinsically disordered proteins (typically biological polyampholytes) expressed in neurons. We describe studies, which reveal an unexpected transition from tightly spaced MT bundles to loose bundles consisting of strings of MTs as the valence of the cationic counter-ion decreases from Z=3 to Z=2. This transition is not predicted by any current theories of polyelectrolytes. Notably, studies of a larger series of divalent counter-ions reveal strong ion specific effects. Divalent counter-ions may either bundle or depolymerize paclitaxel-stabilized MTs. The ion concentration required for depolymerization decreases with increasing atomic number. In a more biologically related system we review synchrotron small angle x-ray scattering (SAXS) studies on the effect of the Tau on the structure of paclitaxel-stabilized MTs. The electrostatic binding of MAP Tau isoforms leads to an increase in the average radius of microtubules with increasing Tau coverage (i.e. a re-distribution of protofilament numbers in MTs). Finally, inspired by MTs as model nanotubes, we briefly describe other more robust lipid-based cylindrical nanostructures, which may have technological applications, for example, in drug encapsulation and delivery.
Collapse
Affiliation(s)
- Cyrus R Safinya
- Materials Department, University of California, Santa Barbara, CA 93106, USA; Physics Department, University of California, Santa Barbara, CA 93106, USA; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA.
| | - Peter J Chung
- Materials Department, University of California, Santa Barbara, CA 93106, USA; Physics Department, University of California, Santa Barbara, CA 93106, USA; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA
| | - Chaeyeon Song
- Materials Department, University of California, Santa Barbara, CA 93106, USA; Physics Department, University of California, Santa Barbara, CA 93106, USA; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA
| | - Kai K Ewert
- Materials Department, University of California, Santa Barbara, CA 93106, USA; Physics Department, University of California, Santa Barbara, CA 93106, USA; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| |
Collapse
|
11
|
|
12
|
Goswami M, Borreguero JM, Pincus PA, Sumpter BG. Surfactant-Mediated Polyelectrolyte Self-Assembly in a Polyelectrolyte–Surfactant Complex. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b02145] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | - Philip A. Pincus
- Department
of Materials Science, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | | |
Collapse
|
13
|
Li J, Wijeratne SS, Qiu X, Kiang CH. DNA under Force: Mechanics, Electrostatics, and Hydration. NANOMATERIALS (BASEL, SWITZERLAND) 2015; 5:246-267. [PMID: 28347009 PMCID: PMC5312857 DOI: 10.3390/nano5010246] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 02/12/2015] [Indexed: 11/16/2022]
Abstract
Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology.
Collapse
Affiliation(s)
- Jingqiang Li
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
| | - Sithara S Wijeratne
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
| | - Xiangyun Qiu
- Department of Physics, George Washington University, Washington, DC 20052, USA.
| | - Ching-Hwa Kiang
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
| |
Collapse
|
14
|
He Z, Chen SJ. Quantifying Coulombic and solvent polarization-mediated forces between DNA helices. J Phys Chem B 2013; 117:7221-7. [PMID: 23701377 DOI: 10.1021/jp4010955] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
One of the fundamental problems in nucleic acids biophysics is to predict the different forces that stabilize nucleic acid tertiary folds. Here we provide a quantitative estimation and analysis for the forces between DNA helices in an ionic solution. Using the generalized Born model and the improved atomistic tightly binding ions model, we evaluate ion correlation and solvent polarization effects in interhelix interactions. The results suggest that hydration, Coulomb correlation and ion entropy act together to cause the repulsion and attraction between nucleic acid helices in Mg(2+) and Mn(2+) solutions, respectively. The theoretical predictions are consistent with experimental findings. Detailed analysis further suggests that solvent polarization and ion correlation both are crucial for the interhelix interactions. The theory presented here may provide a useful framework for systematic and quantitative predictions of the forces in nucleic acids folding.
Collapse
Affiliation(s)
- Zhaojian He
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
| | | |
Collapse
|
15
|
Needleman DJ, Ojeda-Lopez MA, Raviv U, Miller HP, Li Y, Song C, Feinstein SC, Wilson L, Choi MC, Safinya CR. Ion specific effects in bundling and depolymerization of taxol-stabilized microtubules. Faraday Discuss 2013; 166:31-45. [PMID: 24611267 PMCID: PMC3955895 DOI: 10.1039/c3fd00063j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Microtubules (MTs) are nanometer scale hollow cylindrical biological polyelectrolytes. They are assembled from alpha/beta-tubulin dimers, which stack to form protofilaments (PFs) with lateral interactions between PFs resulting in the curved MT. In cells, MTs and their assemblies are critical components in a range of functions from providing tracks for the transport of cargo to forming the spindle structure during mitosis. Previous studies have, shown that while cations with valence equal to or larger than 3+ tend to assemble tight 3D bundles of taxol-stabilized MTs, certain divalent cations induce relatively loose 2D bundles of different symmetry (D. J. Needleman et al., Proc. Natl. Acad. Sci. U. S. A., 2004, 101, 16099). Similarly, divalent cations form 2D bundles of DNA adsorbed on cationic membranes (I. Koltover et al., Proc. Natl. Acad. Sci. U. S. A., 2000, 97, 14046). The bundling behavior for these biological polyelectrolyte systems is qualitatively in agreement with current theory. Here, we present results which show that, unlike the case for DNA adsorbed on cationic membranes, bundling of taxol-stabilized MTs occurs only for certain divalent cations above a critical ion concentration (e.g. Ca2+, Sr2+, Ba2+). Instead, many divalent cations pre-empt the bundling transition and depolymerize taxol-stabilized MTs at a lower counterion concentration. Although previous cryogenic TEM has shown that, in the absence of taxol, Ca2+ depolymerizes MTs assembling in buffers containing GTP (guanosine triphosphate), our finding is surprising given the know stabilizing effects of taxol on GDP (guanosine diphosphate)-MTs. The ion concentration required for MT depolymerization decreases with increasing atomic number for the divalents Mg2+, Mn2+, Co2+, and Zn2+. GdCl3 (3+) is found to be extremely efficient at MT depolymerization requiring ion concentrations of about 1 mM, while oligolysine(2+), is observed not to depolymerize MTs at concentrations as high as 144 mM. The surprising MT depolymerization results are discussed in the context of divalents either disrupting lateral interactions between PFs (which are strengthened for taxol containing beta-tubulin) or interfering with taxol's ability to induce flexibility at the interface between two tubulin dimers in the same PF (which has been recently suggested as a mechanism by which taxol stabilizes MTs post-hydrolysis with the induced flexibility counteracting the kink between GDP-tublin dimers in a PF).
Collapse
Affiliation(s)
- Daniel J. Needleman
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA. ; Fax +1 805 893 8797; Tel +1 805 893 8635
| | - Miguel A. Ojeda-Lopez
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA. ; Fax +1 805 893 8797; Tel +1 805 893 8635
| | - Uri Raviv
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA. ; Fax +1 805 893 8797; Tel +1 805 893 8635
| | - Herbert P. Miller
- Molecular, Cellular, & Developmental Biology Department & Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA
| | - Chaeyeon Song
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Stuart C. Feinstein
- Molecular, Cellular, & Developmental Biology Department & Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Leslie Wilson
- Molecular, Cellular, & Developmental Biology Department & Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Cyrus R. Safinya
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA. ; Fax +1 805 893 8797; Tel +1 805 893 8635
| |
Collapse
|
16
|
Safinya CR, Deek J, Beck R, Jones JB, Leal C, Ewert KK, Li Y. Liquid crystal assemblies in biologically inspired systems. LIQUID CRYSTALS 2013; 40:1748-1758. [PMID: 24558293 PMCID: PMC3927920 DOI: 10.1080/02678292.2013.846422] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this paper, which is part of a collection in honor of Noel Clark's remarkable career on liquid crystal and soft matter research, we present examples of biologically inspired systems, which form liquid crystal (LC) phases with their LC nature impacting biological function in cells or being important in biomedical applications. One area focuses on understanding network and bundle formation of cytoskeletal polyampholytes (filamentous-actin, microtubules, and neurofilaments). Here, we describe studies on neurofilaments (NFs), the intermediate filaments of neurons, which form open network nematic liquid crystal hydrogels in axons. Synchrotron small-angle-x-ray scattering studies of NF-protein dilution experiments and NF hydrogels subjected to osmotic stress show that neurofilament networks are stabilized by competing long-range repulsion and attractions mediated by the neurofilament's polyampholytic sidearms. The attractions are present both at very large interfilament spacings, in the weak sidearm-interpenetrating regime, and at smaller interfilament spacings, in the strong sidearm-interpenetrating regime. A second series of experiments will describe the structure and properties of cationic liposomes (CLs) complexed with nucleic acids (NAs). CL-NA complexes form liquid crystalline phases, which interact in a structure-dependent manner with cellular membranes enabling the design of complexes for efficient delivery of nucleic acid (DNA, RNA) in therapeutic applications.
Collapse
Affiliation(s)
- Cyrus R. Safinya
- Materials, Physics, and Molecular, Cellular, & Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA
| | - Joanna Deek
- Materials, Physics, and Molecular, Cellular, & Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA
- Chemistry and Biochemistry Department, University of California, Santa Barbara, CA 93106, USA
| | - Roy Beck
- Materials, Physics, and Molecular, Cellular, & Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA
| | - Jayna B. Jones
- Materials, Physics, and Molecular, Cellular, & Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA
| | - Cecilia Leal
- Materials, Physics, and Molecular, Cellular, & Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA
| | - Kai K. Ewert
- Materials, Physics, and Molecular, Cellular, & Developmental Biology Departments, University of California, Santa Barbara, CA 93106, USA
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA
| |
Collapse
|
17
|
Strong and Weak Polyelectrolyte Adsorption onto Oppositely Charged Curved Surfaces. POLYELECTROLYTE COMPLEXES IN THE DISPERSED AND SOLID STATE I 2013. [DOI: 10.1007/12_2012_183] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
18
|
Translocation of HIV TAT peptide and analogues induced by multiplexed membrane and cytoskeletal interactions. Proc Natl Acad Sci U S A 2011; 108:16883-8. [PMID: 21969533 DOI: 10.1073/pnas.1108795108] [Citation(s) in RCA: 253] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cell-penetrating peptides (CPPs), such as the HIV TAT peptide, are able to translocate across cellular membranes efficiently. A number of mechanisms, from direct entry to various endocytotic mechanisms (both receptor independent and receptor dependent), have been observed but how these specific amino acid sequences accomplish these effects is unknown. We show how CPP sequences can multiplex interactions with the membrane, the actin cytoskeleton, and cell-surface receptors to facilitate different translocation pathways under different conditions. Using "nunchuck" CPPs, we demonstrate that CPPs permeabilize membranes by generating topologically active saddle-splay ("negative Gaussian") membrane curvature through multidentate hydrogen bonding of lipid head groups. This requirement for negative Gaussian curvature constrains but underdetermines the amino acid content of CPPs. We observe that in most CPP sequences decreasing arginine content is offset by a simultaneous increase in lysine and hydrophobic content. Moreover, by densely organizing cationic residues while satisfying the above constraint, TAT peptide is able to combine cytoskeletal remodeling activity with membrane translocation activity. We show that the TAT peptide can induce structural changes reminiscent of macropinocytosis in actin-encapsulated giant vesicles without receptors.
Collapse
|
19
|
Abstract
We have carried out Brownian dynamics calculations to investigate the effect of DNA-ion interaction on ion transport in a nanopore. We calculated the self-diffusion coefficient of monovalent ions in the presence of DNA in a nanopore and compared the result with that through an open pore, that is, without the presence of DNA. We find that the self-diffusion coefficient of the co-ions is essentially unaffected by the DNA. The self-diffusion coefficient of the counterions, on the other hand, is significantly reduced depending on the ion concentration. At high ion concentration, around 1 M, the effect of DNA on counterion diffusion is relatively small, causing a slight reduction in counterion diffusion coefficient. At low concentrations of a few millimolar, the effect is much larger, resulting in a reduction in counterion diffusion coefficient by a factor of about 2.5. The variation in the self-diffusion of the counterion is well described by accounting for the contributions from two components: the adsorbed counterions and the free counterions. Detailed dynamics of the DNA-counterion interaction is characterized by the varying length of the transient adsorption time of the counterions to the DNA charge sites and the exchange rate with the environment. This variation in counterion adsorption time is attributed to the ionic electric screening effect, which is in turn determined by the ion concentration.
Collapse
Affiliation(s)
- Shengting Cui
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, USA
| |
Collapse
|
20
|
Safinya CR, Raviv U, Needleman DJ, Zidovska A, Choi MC, Ojeda-Lopez MA, Ewert KK, Li Y, Miller HP, Quispe J, Carragher B, Potter CS, Kim MW, Feinstein SC, Wilson L. Nanoscale assembly in biological systems: from neuronal cytoskeletal proteins to curvature stabilizing lipids. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2011; 23:2260-70. [PMID: 21506171 PMCID: PMC3864889 DOI: 10.1002/adma.201004647] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Indexed: 05/30/2023]
Abstract
The review will describe experiments inspired by the rich variety of bundles and networks of interacting microtubules (MT), neurofilaments, and filamentous-actin in neurons where the nature of the interactions, structures, and structure-function correlations remain poorly understood. We describe how three-dimensional (3D) MT bundles and 2D MT bundles may assemble, in cell free systems in the presence of counter-ions, revealing structures not predicted by polyelectrolyte theories. Interestingly, experiments reveal that the neuronal protein tau, an abundant MT-associated-protein in axons, modulates the MT diameter providing insight for the control of geometric parameters in bio- nanotechnology. In another set of experiments we describe lipid-protein-nanotubes, and lipid nano-tubes and rods, resulting from membrane shape evolution processes involving protein templates and curvature stabilizing lipids. Similar membrane shape changes, occurring in cells for the purpose of specific functions, are induced by interactions between membranes and proteins. The biological materials systems described have applications in bio-nanotechnology.
Collapse
Affiliation(s)
- Cyrus R Safinya
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Departments, University of California-Santa Barbara, CA 93106, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Cheng YH, Chen WP, Zheng C, Qu W, Wu H, Shen Z, Liang D, Fan XH, Zhu MF, Zhou QF. Synthesis and Phase Structures of Mesogen-Jacketed Liquid Crystalline Polyelectrolytes and Their Ionic Complexes. Macromolecules 2011. [DOI: 10.1021/ma2001004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan-Hua Cheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, China
| | - Wen-Ping Chen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, China
| | - Cui Zheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Qu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hongliang Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhihao Shen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xing-He Fan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mei-Fang Zhu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, China
| | - Qi-Feng Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
22
|
Mishra A, Tai KP, Schmidt NW, Ouellette AJ, Wong GC. Small-Angle X-ray Scattering Studies of Peptide–Lipid Interactions Using the Mouse Paneth Cell α-Defensin Cryptdin-4. Methods Enzymol 2011; 492:127-49. [DOI: 10.1016/b978-0-12-381268-1.00016-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
23
|
Koh DW, Kim YW, Yi J. Conformations of semiflexible charged chains: an extended bundle versus repulsive coils. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:061801. [PMID: 21230683 DOI: 10.1103/physreve.82.061801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 09/15/2010] [Indexed: 05/30/2023]
Abstract
We consider two interacting semiflexible charged chains of length L(c) under shape fluctuations, where the interplay of electric and mechanical properties is found to yield rigidity-sensitive charge modulation and interdistance-dependent persistence length ℓ(p). The resulting conformation is characterized by equilibrium force between the chains and their fractal dimensions. It turns out that ℓ(p) and L(c) emerge as critical factors to determine the force nature as well as chain shapes. We show that conformational fluctuations cause the repulsion of nonsteric origin, and its competition with charge fluctuation effects yields the interchain force modulated by the length scales and counterion valence. As a result, it is predicted that flexible short chains can be more strongly repulsive than rigid long chains, although they carry smaller amount of net charges.
Collapse
Affiliation(s)
- Dong-Wook Koh
- Department of Physics, Korea University, Seoul 136-713, Korea
| | | | | |
Collapse
|
24
|
Abstract
Understanding and manipulation of the forces assembling DNA/RNA helices have broad implications for biology, medicine, and physics. One subject of significance is the attractive force between dsDNA mediated by polycations of valence ≥ 3. Despite extensive studies, the physical origin of the "like-charge attraction" remains unsettled among competing theories. Here we show that triple-strand DNA (tsDNA), a more highly charged helix than dsDNA, is precipitated by alkaline-earth divalent cations that are unable to condense dsDNA. We further show that our observation is general by examining several cations (Mg(2+), Ba(2+), and Ca(2+)) and two distinct tsDNA constructs. Cation-condensed tsDNA forms ordered hexagonal arrays that redissolve upon adding monovalent salts. Forces between tsDNA helices, measured by osmotic stress, follow the form of hydration forces observed with condensed dsDNA. Probing a well-defined system of point-like cations and tsDNAs with more evenly spaced helical charges, the counterintuitive observation that the more highly charged tsDNA (vs. dsDNA) is condensed by cations of lower valence provides new insights into theories of polyelectrolytes and the biological and pathological roles of tsDNA. Cations and tsDNAs also hold promise as a model system for future studies of DNA-DNA interactions and electrostatic interactions in general.
Collapse
|
25
|
Zanchetta G, Cerbino R. Exploring soft matter with x-rays: from the discovery of the DNA structure to the challenges of free electron lasers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:323102. [PMID: 21386476 DOI: 10.1088/0953-8984/22/32/323102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
X-rays have long been a precious tool for the study of the structure of matter. While the short wavelength makes them ideal for investigating materials down to the atomic scale, their high penetration power allows for the exploration of opaque samples at a multitude of length scales. We give an overview of the x-ray techniques suited for the characterization of soft matter and of their application to systems of current interest. We describe the advantages and limitations of existing x-ray methods and outline the possible developments following the introduction of a new kind of coherent source: the x-ray free electron laser.
Collapse
Affiliation(s)
- Giuliano Zanchetta
- Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, I-20133, Milano, Italy.
| | | |
Collapse
|
26
|
Dias RS, Pais AACC. Polyelectrolyte condensation in bulk, at surfaces, and under confinement. Adv Colloid Interface Sci 2010; 158:48-62. [PMID: 20347064 DOI: 10.1016/j.cis.2010.02.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 02/05/2010] [Accepted: 02/14/2010] [Indexed: 11/18/2022]
Abstract
In this review we discuss recent results from computer simulations based on coarse-grained polyion models representing aqueous solutions of polyelectrolytes. The focus will be directed to the conformation of the polyions and, in particular, their condensation in bulk, induced by multivalent ions and oppositely charged polyelectrolytes, at responsive surfaces and under confinement.
Collapse
Affiliation(s)
- R S Dias
- Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | | |
Collapse
|
27
|
Landy J, Rudnick J. Symmetries of interacting helices of charge. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:061918. [PMID: 20866451 DOI: 10.1103/physreve.81.061918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Indexed: 05/29/2023]
Abstract
We analytically examine the pair interaction for parallel discrete helices of charge. Symmetry arguments allow for the free energy to be decomposed into a sum of terms, each of which has an intuitive geometric interpretation. Truncated Fourier expansions of these terms are shown to provide effective free energy expressions that are valid under very general circumstances. These expressions are used to briefly examine and characterize the azimuthal interactions within F-actin and A-DNA aggregates.
Collapse
Affiliation(s)
- Jonathan Landy
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095-1547, USA.
| | | |
Collapse
|
28
|
Mylon SE, Rinciog CI, Schmidt N, Gutierrez L, Wong GCL, Nguyen TH. Influence of salts and natural organic matter on the stability of bacteriophage MS2. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1035-1042. [PMID: 19775143 DOI: 10.1021/la902290t] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The stability of functionalized nanoparticles generally results from both steric and electrostatic interactions. Viruses like bacteriophage MS2 have adopted similar strategies for stability against aggregation, including a net negative charge under natural water conditions and using polypeptides that form loops extending from the surface of the protein capsid for stabilization. In natural systems, dissolved organic matter can adsorb to and effectively functionalize nanoparticle surfaces, affecting the fate and transport of these nanoparticles. We used time-resolved dynamic light scattering to measure the aggregation kinetics of a model virus, bacteriophage MS2, across a range of solution chemistries to determine what factors might destabilize viruses in aquatic systems. In monovalent electrolytes (LiCl, NaCl, and KCl), aggregation of MS2 could not be induced within a reasonable kinetic time frame, and MS2 was stable even at salt concentrations greater than 1.0 M. Aggregation of MS2 could be induced in divalent electrolytes when we employed Ca(2+). This trend was also observed in solutions containing 10 mg/L Suwannee River organic matter (SROM) reference material. Even at Ca(2+) concentrations as high 200 mM, diffusion-controlled aggregation was never achieved, demonstrating an additional barrier to aggregation. These results were confirmed by small-angle X-ray scattering experiments, which indicate a transition from repulsive to attractive interactions between MS2 virus particles as monovalent salts are replaced by divalent salts.
Collapse
Affiliation(s)
- Steven E Mylon
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, USA
| | | | | | | | | | | |
Collapse
|
29
|
Wei YF, Hsiao PY. Effect of chain stiffness on ion distributions around a polyelectrolyte in multivalent salt solutions. J Chem Phys 2010; 132:024905. [DOI: 10.1063/1.3284785] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
|
30
|
Landy J. Modulation effects within the mean-field theory of electrolyte solutions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:011401. [PMID: 20365367 DOI: 10.1103/physreve.81.011401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Indexed: 05/29/2023]
Abstract
The consequences of source charge and surface modulation are studied within the framework of the Poisson-Boltzmann theory of electrolyte solutions. Through a consideration of various examples, it is found that inherent modulation can lead to both like-charge attraction and overcharging effects.
Collapse
Affiliation(s)
- Jonathan Landy
- Department of Physics and Astronomy, University of California-Los Angeles, Los Angeles, California 90095-1547, USA.
| |
Collapse
|
31
|
Arginine-rich cell-penetrating peptides. FEBS Lett 2009; 584:1806-13. [DOI: 10.1016/j.febslet.2009.11.046] [Citation(s) in RCA: 388] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/09/2009] [Accepted: 11/11/2009] [Indexed: 11/17/2022]
|
32
|
Avendaño C, Gil-Villegas A, González-Tovar E. A Monte Carlo simulation study of binary mixtures of charged hard spherocylinders and charged hard spheres. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.01.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
33
|
Park HS, Agarwal A, Kotov NA, Lavrentovich OD. Controllable side-by-side and end-to-end assembly of Au nanorods by lyotropic chromonic materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:13833-7. [PMID: 19053632 DOI: 10.1021/la803363m] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We present a simple and universal technique for assembling gold nanorods (NRs) using self-assembled stacks of lyotropic chromonic materials, without covalent bonding between NRs and the linking agent. The anisotropic electrostatic interaction between the chromonic stacks and NRs allows one to achieve either side-by-side or end-to-end assembly, depending on the surface charge of NRs. The assembled superstructures are stable within an extended temperature range; the degree of NR aggregation can be controlled by a number of factors influencing the self-assembly of chromonic materials, such as the concentration and pH of the solution.
Collapse
Affiliation(s)
- Heung-Shik Park
- Liquid Crystal Institute and Chemical Physics Interdisciplinary Program, Kent State University, Kent, Ohio 44242, USA
| | | | | | | |
Collapse
|
34
|
Purdy Drew KR, Sanders LK, Culumber ZW, Zribi O, Wong GCL. Cationic Amphiphiles Increase Activity of Aminoglycoside Antibiotic Tobramycin in the Presence of Airway Polyelectrolytes. J Am Chem Soc 2008; 131:486-93. [DOI: 10.1021/ja803925n] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kirstin R. Purdy Drew
- Departments of Materials Science and Engineering, Animal Biology, Physics, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Lori K. Sanders
- Departments of Materials Science and Engineering, Animal Biology, Physics, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Zachary W. Culumber
- Departments of Materials Science and Engineering, Animal Biology, Physics, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Olena Zribi
- Departments of Materials Science and Engineering, Animal Biology, Physics, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Gerard C. L. Wong
- Departments of Materials Science and Engineering, Animal Biology, Physics, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| |
Collapse
|
35
|
Qiu X, Andresen K, Lamb JS, Kwok LW, Pollack L. Abrupt transition from a free, repulsive to a condensed, attractive DNA phase, induced by multivalent polyamine cations. PHYSICAL REVIEW LETTERS 2008; 101:228101. [PMID: 19113524 PMCID: PMC2843915 DOI: 10.1103/physrevlett.101.228101] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Indexed: 05/18/2023]
Abstract
We have investigated the energetics of DNA condensation by multivalent polyamine cations. Solution small angle x-ray scattering was used to monitor interactions between short 25 base pair dsDNA strands in the free supernatant DNA phase that coexists with the condensed DNA phase. Interestingly, when tetravalent spermine is used, significant inter-DNA repulsion is observed in the free phase, in contrast with the presumed inter-DNA attraction in the coexisting condensed phase. DNA condensation thus appears to be a discrete, first-order-like, transition from a repulsive gaseous to an attractive condensed solid phase, in accord with the reported all-or-none condensation of giant DNA. We further quantify the electrostatic repulsive potentials in the free DNA phase and estimate the number of additional spermine cations that bind to DNA upon condensation.
Collapse
Affiliation(s)
- Xiangyun Qiu
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | | | | | | | | |
Collapse
|
36
|
Dai L, Mu Y, Nordenskiöld L, van der Maarel JRC. Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules. PHYSICAL REVIEW LETTERS 2008; 100:118301. [PMID: 18517834 DOI: 10.1103/physrevlett.100.118301] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Indexed: 05/26/2023]
Abstract
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.
Collapse
Affiliation(s)
- Liang Dai
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542
| | | | | | | |
Collapse
|
37
|
Sanders LK, Xian W, Guáqueta C, Strohman MJ, Vrasich CR, Luijten E, Wong GCL. Control of electrostatic interactions between F-actin and genetically modified lysozyme in aqueous media. Proc Natl Acad Sci U S A 2007; 104:15994-9. [PMID: 17911256 PMCID: PMC2042150 DOI: 10.1073/pnas.0705898104] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim for deterministic control of the interactions between macroions in aqueous media has motivated widespread experimental and theoretical work. Although it has been well established that like-charged macromolecules can aggregate under the influence of oppositely charged condensing agents, the specific conditions for the stability of such aggregates can only be determined empirically. We examine these conditions, which involve an interplay of electrostatic and osmotic effects, by using a well defined model system composed of F-actin, an anionic rod-like polyelectrolyte, and lysozyme, a cationic globular protein with a charge that can be genetically modified. The structure and stability of actin-lysozyme complexes for different lysozyme charge mutants and salt concentrations are examined by using synchrotron x-ray scattering and molecular dynamics simulations. We provide evidence that supports a structural transition from columnar arrangements of F-actin held together by arrays of lysozyme at the threefold interstitial sites of the actin sublattice to marginally stable complexes in which lysozyme resides at twofold bridging sites between actin. The reduced stability arises from strongly reduced partitioning of salt between the complex and the surrounding solution. Changes in the stability of actin-lysozyme complexes are of biomedical interest because their formation has been reported to contribute to the persistence of airway infections in cystic fibrosis by sequestering antimicrobials such as lysozyme. We present x-ray microscopy results that argue for the existence of actin-lysozyme complexes in cystic fibrosis sputum and demonstrate that, for a wide range of salt conditions, charge-reduced lysozyme is not sequestered in ordered complexes while retaining its bacterial killing activity.
Collapse
Affiliation(s)
| | - Wujing Xian
- Departments of *Materials Science and Engineering
| | | | | | | | - Erik Luijten
- Departments of *Materials Science and Engineering
- Physics, and
- The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL 61801-2920
- To whom correspondence may be addressed at:
Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign, 1304 W. Green Street, Urbana, IL 61801-2920. E-mail: or
| | - Gerard C. L. Wong
- Departments of *Materials Science and Engineering
- Physics, and
- Bioengineering
- The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL 61801-2920
- To whom correspondence may be addressed at:
Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign, 1304 W. Green Street, Urbana, IL 61801-2920. E-mail: or
| |
Collapse
|
38
|
Qiu X, Andresen K, Kwok LW, Lamb JS, Park HY, Pollack L. Inter-DNA attraction mediated by divalent counterions. PHYSICAL REVIEW LETTERS 2007; 99:038104. [PMID: 17678334 DOI: 10.1103/physrevlett.99.038104] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Indexed: 05/16/2023]
Abstract
Can nonspecifically bound divalent counterions induce attraction between DNA strands? Here, we present experimental evidence demonstrating attraction between short DNA strands mediated by Mg2+ ions. Solution small angle x-ray scattering data collected as a function of DNA concentration enable model independent extraction of the second virial coefficient. As the [Mg2+] increases, this coefficient turns from positive to negative reflecting the transition from repulsive to attractive inter-DNA interaction. This surprising observation is corroborated by independent light scattering experiments. The dependence of the observed attraction on experimental parameters including DNA length provides valuable clues to its origin.
Collapse
Affiliation(s)
- Xiangyun Qiu
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | | | | | | | | | | |
Collapse
|