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Wang Z, Zhang S, Xu Q, Li Z, Gu X, Wood K, García Sakai V, Wan Q, Chu XQ. Experimental Evidence for the Role of Dynamics in pH-Dependent Enzymatic Activity. J Phys Chem B 2024; 128:5814-5822. [PMID: 38726956 DOI: 10.1021/acs.jpcb.4c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Enzymatic activity is heavily influenced by pH, but the rationale for the dynamical mechanism of pH-dependent enzymatic activity has not been fully understood. In this work, combined neutron scattering techniques, including quasielastic neutron scattering (QENS) and small angle neutron scattering (SANS), are used to study the structural and dynamic changes of a model enzyme, xylanase, under different pH and temperature environments. The QENS results reveal that xylanase at optimal pH exhibits faster relaxational dynamics and a lower energy barrier between conformational substates. The SANS results demonstrate that pH affects both xylanase's stability and monodispersity. Our findings indicate that enzymes have optimized stability and function under their optimal pH conditions, with both structure and dynamics being affected. The current study offers valuable insights into enzymatic functionality mechanisms, allowing for broad industrial applications.
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Affiliation(s)
- Zhixin Wang
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Shengkai Zhang
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Institute of Advanced Science Facilities, Shenzhen 518107, China
| | - Qin Xu
- College of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihong Li
- College of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xudong Gu
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organization, Lucas Heights, NSW 2234, Australia
| | - Victoria García Sakai
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Qun Wan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizer, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiang-Qiang Chu
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
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2
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Ren H, Chen H, Kang Y, Liu W, Liu Y, Tao F, Miao S, Zhang Y, Liu Q, Dong M, Liu Y, Liu B, Yang P. Non-fibril amyloid aggregation at the air/water interface: self-adaptive pathway resulting in a 2D Janus nanofilm. Chem Sci 2024; 15:8946-8958. [PMID: 38873054 PMCID: PMC11168098 DOI: 10.1039/d4sc00560k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/27/2024] [Indexed: 06/15/2024] Open
Abstract
The amyloid states of proteins are implicated in several neurodegenerative diseases and bioadhesion processes. However, the classical amyloid fibrillization mechanism fails to adequately explain the formation of polymorphic aggregates and their adhesion to various surfaces. Herein, we report a non-fibril amyloid aggregation pathway, with disulfide-bond-reduced lysozyme (R-Lyz) as a model protein under quasi-physiological conditions. Very different from classical fibrillization, this pathway begins with the air-water interface (AWI) accelerated oligomerization of unfolded full-length protein, resulting in unique plate-like oligomers with self-adaptive ability, which can adjust their conformations to match various interfaces such as the asymmetric AWI and amyloid-protein film surface. The pathway enables a stepwise packing of the plate-like oligomers into a 2D Janus nanofilm, exhibiting a divergent distribution of hydrophilic/hydrophobic residues on opposite sides of the nanofilm. The resulting Janus nanofilm possesses a top-level Young's modulus (8.3 ± 0.6 GPa) among amyloid-based materials and exhibits adhesive strength two times higher (145 ± 81 kPa) than that of barnacle cement. Furthermore, we found that such an interface-directed pathway exists in several amyloidogenic proteins with a similar self-adaptive 2D-aggregation process, including bovine serum albumin, insulin, fibrinogen, hemoglobin, lactoferrin, and ovalbumin. Thus, our findings on the non-fibril self-adaptive mechanism for amyloid aggregation may shed light on polymorphic amyloid assembly and their adhesions through an alternative pathway.
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Affiliation(s)
- Hao Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Huan Chen
- First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University Xi'an 710061 China
| | - Yu Kang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 China
| | - Wei Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Yongchun Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Fei Tao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Shuting Miao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Yingying Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Qian Liu
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Aarhus C Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Aarhus C Denmark
| | - Yonggang Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 China
| | - Bing Liu
- First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University Xi'an 710061 China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
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3
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Sun S, Zhu R, Zhu M, Wang Q, Li N, Yang B. Visualization of conformational transition of GRP94 in solution. Life Sci Alliance 2024; 7:e202302051. [PMID: 37949474 PMCID: PMC10638095 DOI: 10.26508/lsa.202302051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
GRP94, an ER paralog of the heat-shock protein 90 family, binds and hydrolyses ATP to chaperone the folding and maturation of its selected clients. Compared with other hsp90 proteins, the in-solution conformational dynamics of GRP94 along the ATP hydrolysis cycle are less understood, hindering our understanding of its chaperoning mechanism. Leveraging small-angle X-ray scattering, negative-staining EM, and hydrogen-deuterium exchange coupled mass-spec, here we show that in its apo form, ∼60% of mouse GRP94 (mGRP94) populates an "extended" conformation, whereas the rest exist in either "close V" or "twist V" like "compact" conformations. Different from other hsp90 proteins, the presence of AMPPNP only impacts the relative abundance of the two compact conformations, rather than shifting the equilibrium between the "extended" and "compact" conformations of mGRP94. HDX-MS study of apo, AMPPNP-bound, and ADP-bound mGRP94 suggests a conformational transition from "twist V" to "close V" upon ATP binding and a back transition from "close V" to "twist V" upon ATP hydrolysis. These results illustrate the dissimilarities of GRP94 in conformation transition during ATP hydrolysis from other hsp90 paralogs.
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Affiliation(s)
- Shangwu Sun
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Rui Zhu
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mengyao Zhu
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qi Wang
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), Chinese Academy of Sciences, Shanghai, China
| | - Bei Yang
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- https://ror.org/030bhh786 Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
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4
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Hopkins JB. BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis. J Appl Crystallogr 2024; 57:194-208. [PMID: 38322719 PMCID: PMC10840314 DOI: 10.1107/s1600576723011019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/21/2023] [Indexed: 02/08/2024] Open
Abstract
BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI; updated automated Guinier fitting and D max finding algorithms; automated series (e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares (REGALS); creation of electron-density reconstructions using electron density via solution scattering (DENSS); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.
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Affiliation(s)
- Jesse B. Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
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5
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Choi S, Park S, Kim J, Kim H, Cho S, Kim S, Park J, Kim C. X-ray free-electron laser induced acoustic microscopy (XFELAM). PHOTOACOUSTICS 2024; 35:100587. [PMID: 38312809 PMCID: PMC10835452 DOI: 10.1016/j.pacs.2024.100587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/06/2024]
Abstract
The X-ray free-electron laser (XFEL) has remarkably advanced X-ray imaging technology and enabled important scientific achievements. The XFEL's extremely high power, short pulse width, low emittance, and high coherence make possible such diverse imaging techniques as absorption/emission spectroscopy, diffraction imaging, and scattering imaging. Here, we demonstrate a novel XFEL-based imaging modality that uses the X-ray induced acoustic (XA) effect, which we call X-ray free-electron laser induced acoustic microscopy (XFELAM). Initially, we verified the XA effect by detecting XA signals from various materials, then we validated the experimental results with simulation outcomes. Next, in resolution experiments, we successfully imaged a patterned tungsten target with drilled various-sized circles at a spatial resolution of 7.8 ± 5.1 µm, which is the first micron-scale resolution achieved by XA imaging. Our results suggest that the novel XFELAM can expand the usability of XFEL in various areas of fundamental scientific research.
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Affiliation(s)
- Seongwook Choi
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Sinyoung Park
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Jiwoong Kim
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Hyunhee Kim
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Seonghee Cho
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Sunam Kim
- Pohang Accelerator Laboratory, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Jaeku Park
- Pohang Accelerator Laboratory, 77 Cheongam-ro, Pohang 37673, Republic of Korea
| | - Chulhong Kim
- Pohang University of Science and Technology (POSTECH), Medical Device Innovation Center, Department of Electrical Engineering, Convergence IT Engineering, Mechanical Engineering, Medical Science and Engineering, 77 Cheongam-ro, Pohang 37673, Republic of Korea
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6
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Saini M, Upadhyay N, Dhiman K, Manjhi SK, Kattuparambil AA, Ghoshal A, Arya R, Dey SK, Sharma A, Aduri R, Thelma BK, Ashish F, Kundu S. ARL15, a GTPase implicated in rheumatoid arthritis, potentially repositions its truncated N-terminus as a function of guanine nucleotide binding. Int J Biol Macromol 2024; 254:127898. [PMID: 37939768 DOI: 10.1016/j.ijbiomac.2023.127898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/21/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
The ADP ribosylation factor like protein 15 (ARL15) gene encodes for an uncharacterized GTPase associated with rheumatoid arthritis (RA) and other metabolic disorders. Investigation of the structural and functional attributes of ARL15 is important to position the protein as a potential drug target. Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. The equilibrium dissociation constant (Kd) of GTP binding with ARL15 was estimated to be about eight-fold higher than that of GDP. Small Angle X-ray Scattering (SAXS) data indicated that in solution, the apo state of monomeric ARL15 adopts a shape characterized by a globe of maximum linear dimension (Dmax) of 6.1 nm, and upon binding to GTP or GDP, the vector distribution profile changes to peak-n-tail shoulder with Dmax extended to 7.6 and 7.7 nm, respectively. Structure restoration using a sequence-based template and experimental SAXS data provided the first visual insight revealing that the folded N-terminal in the unbound state of the protein may toggle open upon binding to guanine nucleotides. The conformational dynamics observed in the N-terminal region offer a scope to develop drugs that target this unique GTPase, potentially providing treatments for a range of metabolic disorders.
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Affiliation(s)
- Manisha Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Neelam Upadhyay
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Kanika Dhiman
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Satish Kumar Manjhi
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - Aman Achutan Kattuparambil
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - Antara Ghoshal
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Sanjay Kumar Dey
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Aditya Sharma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Raviprasad Aduri
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Fnu Ashish
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India; Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India.
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7
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Hopkins JB. BioXTAS RAW 2: new developments for a free open-source program for small angle scattering data reduction and analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559353. [PMID: 37808703 PMCID: PMC10557611 DOI: 10.1101/2023.09.25.559353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
BioXTAS RAW is a free, open-source program for reduction, analysis and modelling of biological small angle scattering data. Here, the new developments in RAW version 2 are described. These include: improved data reduction using pyFAI; updated automated Guinier fitting and Dmax finding algorithms; automated series (e.g. SEC-SAXS) buffer and sample region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using REGALS; creation of electron density reconstructions via DENSS; a comparison window showing residuals, ratios, and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. In addition, there is now a RAW API, which can be used without the GUI, providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.
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Affiliation(s)
- Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
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8
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Golub M, Pieper J. Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods. Molecules 2023; 28:7414. [PMID: 37959833 PMCID: PMC10650700 DOI: 10.3390/molecules28217414] [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: 09/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Utilized for gaining structural insights, small-angle neutron and X-ray scattering techniques (SANS and SAXS, respectively) enable an examination of biomolecules, including photosynthetic pigment-protein complexes, in solution at physiological temperatures. These methods can be seen as instrumental bridges between the high-resolution structural information achieved by crystallography or cryo-electron microscopy and functional explorations conducted in a solution state. The review starts with a comprehensive overview about the fundamental principles and applications of SANS and SAXS, with a particular focus on the recent advancements permitting to enhance the efficiency of these techniques in photosynthesis research. Among the recent developments discussed are: (i) the advent of novel modeling tools whereby a direct connection between SANS and SAXS data and high-resolution structures is created; (ii) the employment of selective deuteration, which is utilized to enhance spatial selectivity and contrast matching; (iii) the potential symbioses with molecular dynamics simulations; and (iv) the amalgamations with functional studies that are conducted to unearth structure-function relationships. Finally, reference is made to time-resolved SANS/SAXS experiments, which enable the monitoring of large-scale structural transformations of proteins in a real-time framework.
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Affiliation(s)
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald Str. 1, 50411 Tartu, Estonia;
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9
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Gottipati K, McNeme SC, Tipo J, White MA, Choi K. Structural basis for cloverleaf RNA-initiated viral genome replication. Nucleic Acids Res 2023; 51:8850-8863. [PMID: 37486760 PMCID: PMC10484678 DOI: 10.1093/nar/gkad618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023] Open
Abstract
The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CDpro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CDpro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem-loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.
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Affiliation(s)
- Keerthi Gottipati
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA
| | - Sean C McNeme
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Jerricho Tipo
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA
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10
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Tants JN, Schlundt A. Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA. Chembiochem 2023; 24:e202300110. [PMID: 37466350 DOI: 10.1002/cbic.202300110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/22/2023] [Indexed: 07/20/2023]
Abstract
RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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11
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Hamley IW, Castelletto V. Small-angle scattering techniques for peptide and peptide hybrid nanostructures and peptide-based biomaterials. Adv Colloid Interface Sci 2023; 318:102959. [PMID: 37473606 DOI: 10.1016/j.cis.2023.102959] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
The use of small-angle scattering (SAS) in the study of the self-assembly of peptides and peptide conjugates (lipopeptides, polymer-peptide conjugates and others) is reviewed, highlighting selected research that illustrates different methods and analysis techniques. Both small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) are considered along with examples that exploit their unique capabilities. For SAXS, this includes the ability to perform rapid measurements enabling high throughput or fast kinetic studies and measurements under dilute conditions. For SANS, contrast variation using H2O/D2O mixtures enables the study of peptides interacting with lipids and TR-SANS (time-resolved SANS) studies of exchange kinetics and/or peptide-induced structural changes. Examples are provided of studies measuring form factors of different self-assembled structures (micelles, fibrils, nanotapes, nanotubes etc) as well as structure factors from ordered phases (lyotropic mesophases), peptide gels and hybrid materials such as membranes formed by mixing peptides with polysaccharides or peptide/liposome mixtures. SAXS/WAXS (WAXS: wide-angle x-ray scattering) on peptides and peptide hybrids is also discussed, and the review concludes with a perspective on potential future directions for research in the field.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.
| | - Valeria Castelletto
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
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12
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Sonje J, Thakral S, Krueger S, Suryanarayanan R. Enabling Efficient Design of Biological Formulations Through Advanced Characterization. Pharm Res 2023; 40:1459-1477. [PMID: 36959413 DOI: 10.1007/s11095-023-03495-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/01/2023] [Indexed: 03/25/2023]
Abstract
The present review summarizes the use of differential scanning calorimetry (DSC) and scattering techniques in the context of protein formulation design and characterization. The scattering techniques include wide angle X-ray diffractometry (XRD), small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS). While DSC is valuable for understanding thermal behavior of the excipients, XRD provides critical information about physical state of solutes during freezing, annealing and in the final lyophile. However, as these techniques lack the sensitivity to detect biomolecule-related transitions, complementary characterization techniques such as small-angle scattering can provide valuable insights.
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Affiliation(s)
- Jayesh Sonje
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
- BioTherapeutics, Pharmaceutical Sciences, Pfizer Inc., 1 Burtt Road, Andover, USA
| | - Seema Thakral
- Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Susan Krueger
- Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Raj Suryanarayanan
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA.
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13
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Xu X, Wang X, Cui X, Jia B, Xu B, Sun J. Dispersion Performances of Naphthalimides Doped in Dual Temperature- and pH-Sensitive Poly (N-Isopropylacrylamide-co-acrylic Acid) Shell Assembled with Vinyl-Modified Mesoporous SiO 2 Core for Fluorescence Cell Imaging. Polymers (Basel) 2023; 15:polym15102339. [PMID: 37242914 DOI: 10.3390/polym15102339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/28/2023] Open
Abstract
Developing effective intelligent nanocarriers is highly desirable for fluorescence imaging and therapeutic applications but remains challenging. Using a vinyl-grafted BMMs (bimodal mesoporous SiO2 materials) as a core and PAN ((2-aminoethyl)-6-(dimethylamino)-1H-benzo[de]isoquinoline-1,3(2H)-dione))-dispersed dual pH/thermal-sensitive poly(N-isopropylacrylamide-co-acrylic acid) as a shell, PAN@BMMs with strong fluorescence and good dispersibility were prepared. Their mesoporous features and physicochemical properties were extensively characterized via XRD patterns, N2 adsorption-desorption analysis, SEM/TEM images, TGA profiles, and FT-IR spectra. In particular, their mass fractal dimension (dm) features based on SAXS patterns combined with fluorescence spectra were successfully obtained to evaluate the uniformity of the fluorescence dispersions, showing that the dm values increased from 2.49 to 2.70 with an increase of the AN-additive amount from 0.05 to 1%, along with the red shifting of their fluorescent emission wavelength from 471 to 488 nm. The composite (PAN@BMMs-I-0.1) presented a densification trend and a slight decrease in peak (490 nm) intensity during the shrinking process. Its fluorescent decay profiles confirmed two fluorescence lifetimes of 3.59 and 10.62 ns. The low cytotoxicity obtained via in vitro cell survival assay and the efficient green imaging performed via HeLa cell internalization suggested that the smart PAN@BMM composites are potential carriers for in vivo imaging and therapy.
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Affiliation(s)
- Xiaohuan Xu
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Xiaoli Wang
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Xueqing Cui
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Bingying Jia
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Bang Xu
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Jihong Sun
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
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14
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Rastogi P, Honecker D, Alba Venero D, Mahmoudi N, Kaisare NS, Basavaraj MG. Investigation of Nanostructure and Interactions in Water-in-Xylene Microemulsions Using Small-Angle X-ray and Neutron Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4701-4711. [PMID: 36940278 DOI: 10.1021/acs.langmuir.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The ability to modulate the size, the nanostructure, and the macroscopic properties of water-in-oil microemulsions is useful for a variety of technological scenarios. To date, diverse structures of water-in-alkane microemulsions stabilized by sodium bis(2-ethylhexyl) sulfosuccinate (AOT) have been extensively studied. Even though the decisive parameter which dictates the phase behavior of micremulsions is the nature of the continuous phase, relatively very few reports are available on the structure and interactions in the microemulsions of aromatic oil. Here, we present a fundamental investigation on water-in-xylene microemulsions using small-angle neutron scattering (SANS) at a fixed molar ratio (ω) of water to AOT. We elucidate the microstructural changes in the water-AOT-xylene ternary system at dilute volume fractions (Φ = 0.005, 0.01, 0.03), where the droplet-droplet interactions are absent, to moderately concentrated systems (Φ = 0.05, 0.10, 0.15, and 0.20), where colloidal interactions become important. We also characterize the reverse microemulsions (RMs) for thermally induced microstructural changes at six different temperatures from 20 to 50 °C. Depending on the magnitude of Φ, the scattering data is found to be well described by considering the RMs as a dispersion of droplets (with a Schulz polydispersity) which interact as sticky hard spheres. We show that while the droplet diameter remains almost constant with increase in the volume fraction, the attractive interactions become prominent, much like the trends observed for water-in-alkane microemulsions. With increase in temperature, the RMs showed a marginal decrease in the droplet size but no pronounced dependence on the interactions was observed with the overall structure remaining intact. The fundamental study on a model system presented in this work is key to understanding the phase behavior of multiple component microemulsions as well as their design for applications at higher temperatures, where the structure of most RMs breaks down.
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Affiliation(s)
- Preetika Rastogi
- Department of Chemical Engineering, Indian Institute of Technology, Madras, Chennai 600036, Tamil Nadu, India
| | - Dirk Honecker
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Diego Alba Venero
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Najet Mahmoudi
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Niket S Kaisare
- Department of Chemical Engineering, Indian Institute of Technology, Madras, Chennai 600036, Tamil Nadu, India
| | - Madivala G Basavaraj
- Department of Chemical Engineering, Indian Institute of Technology, Madras, Chennai 600036, Tamil Nadu, India
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15
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Heil C, Ma Y, Bharti B, Jayaraman A. Computational Reverse-Engineering Analysis for Scattering Experiments for Form Factor and Structure Factor Determination (" P( q) and S( q) CREASE"). JACS AU 2023; 3:889-904. [PMID: 37006757 PMCID: PMC10052275 DOI: 10.1021/jacsau.2c00697] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 05/11/2023]
Abstract
In this paper, we present an open-source machine learning (ML)-accelerated computational method to analyze small-angle scattering profiles [I(q) vs q] from concentrated macromolecular solutions to simultaneously obtain the form factor P(q) (e.g., dimensions of a micelle) and the structure factor S(q) (e.g., spatial arrangement of the micelles) without relying on analytical models. This method builds on our recent work on Computational Reverse-Engineering Analysis for Scattering Experiments (CREASE) that has either been applied to obtain P(q) from dilute macromolecular solutions (where S(q) ∼1) or to obtain S(q) from concentrated particle solutions when P(q) is known (e.g., sphere form factor). This paper's newly developed CREASE that calculates P(q) and S(q), termed as "P(q) and S(q) CREASE", is validated by taking as input I(q) vs q from in silico structures of known polydisperse core(A)-shell(B) micelles in solutions at varying concentrations and micelle-micelle aggregation. We demonstrate how "P(q) and S(q) CREASE" performs if given two or three of the relevant scattering profiles-I total(q), I A(q), and I B(q)-as inputs; this demonstration is meant to guide experimentalists who may choose to do small-angle X-ray scattering (for total scattering from the micelles) and/or small-angle neutron scattering with appropriate contrast matching to get scattering solely from one or the other component (A or B). After validation of "P(q) and S(q) CREASE" on in silico structures, we present our results analyzing small-angle neutron scattering profiles from a solution of core-shell type surfactant-coated nanoparticles with varying extents of aggregation.
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Affiliation(s)
- Christian
M. Heil
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
| | - Yingzhen Ma
- Cain
Department of Chemical Engineering, Louisiana
State University, 3307 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Bhuvnesh Bharti
- Cain
Department of Chemical Engineering, Louisiana
State University, 3307 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, 201 DuPont
Hall, Newark, Delaware 19716, United States
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16
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Golub M, Moldenhauer M, Matsarskaia O, Martel A, Grudinin S, Soloviov D, Kuklin A, Maksimov EG, Friedrich T, Pieper J. Stages of OCP-FRP Interactions in the Regulation of Photoprotection in Cyanobacteria, Part 2: Small-Angle Neutron Scattering with Partial Deuteration. J Phys Chem B 2023; 127:1901-1913. [PMID: 36815674 DOI: 10.1021/acs.jpcb.2c07182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We used small-angle neutron scattering partially coupled with size-exclusion chromatography to unravel the solution structures of two variants of the Orange Carotenoid Protein (OCP) lacking the N-terminal extension (OCP-ΔNTE) and its complex formation with the Fluorescence Recovery Protein (FRP). The dark-adapted, orange form OCP-ΔNTEO is fully photoswitchable and preferentially binds the pigment echinenone. Its complex with FRP consists of a monomeric OCP component, which closely resembles the compact structure expected for the OCP ground state, OCPO. In contrast, the pink form OCP-ΔNTEP, preferentially binding the pigment canthaxanthin, is mostly nonswitchable. The pink OCP form appears to occur as a dimer and is characterized by a separation of the N- and C-terminal domains, with the canthaxanthin embedded only into the N-terminal domain. Therefore, OCP-ΔNTEP can be viewed as a prototypical model system for the active, spectrally red-shifted state of OCP, OCPR. The dimeric structure of OCP-ΔNTEP is retained in its complex with FRP. Small-angle neutron scattering using partially deuterated OCP-FRP complexes reveals that FRP undergoes significant structural changes upon complex formation with OCP. The observed structures are assigned to individual intermediates of the OCP photocycle in the presence of FRP.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Marcus Moldenhauer
- Institute of Chemistry PC 14, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Olga Matsarskaia
- Institut Laue-Langevin, Avenue des Martyrs 71, 38042 Cedex 9 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, Avenue des Martyrs 71, 38042 Cedex 9 Grenoble, France
| | - Sergei Grudinin
- Université Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000 Grenoble, France
| | - Dmytro Soloviov
- Faculty of Physics, Adam Mickiewicz University, ul. Wieniawskiego 1, 61-712 Poznan, Poland.,Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kirova 36a, 07270 Chornobyl, Ukraine
| | - Alexander Kuklin
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia.,Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - Eugene G Maksimov
- Department of Biophysics, M. V. Lomonosov Moscow State University, Vorob'jovy Gory 1-12, 119899 Moscow, Russia
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
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17
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Cholesterol stabilization of phospholipid vesicles against bile-induced solubilization. Chem Phys Lipids 2023; 252:105289. [PMID: 36813145 DOI: 10.1016/j.chemphyslip.2023.105289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/03/2022] [Accepted: 02/17/2023] [Indexed: 02/22/2023]
Abstract
Sphingomyelin (SM) and cholesterol complex to form functional liquid-ordered (Lo) domains. It has been suggested that the detergent resistance of these domains plays a key role during gastrointestinal digestion of the milk fat globule membrane (MFGM), which is rich in both SM and cholesterol. Small-angle X-ray scattering was employed to determine the structural alterations that occur when milk sphingomyelin (MSM)/cholesterol, egg sphingomyelin (ESM)/cholesterol, soy phosphatidylcholine (SPC)/cholesterol, and milk fat globule membrane (MFGM) phospholipid/cholesterol model bilayer systems were incubated with bovine bile under physiological conditions. The persistence of diffraction peaks was indicative of multilamellar vesicles of MSM with cholesterol concentrations > 20 % mol, and also for ESM with or without cholesterol. The complexation of ESM with cholesterol is therefore capable of inhibiting the resulting vesicles from disruption by bile at lower cholesterol concentrations than MSM/cholesterol. After subtraction of background scattering by large aggregates in the bile, a Guinier fitting was used to determine changes in the radii of gyration (Rgs) over time for the biliary mixed micelles after mixing the vesicle dispersions with bile. Swelling of the micelles by phospholipid solubilization from vesicles was a function of cholesterol concentration, with less swelling of the micelles occurring as the cholesterol concentration was increased. With 40% mol cholesterol, the Rgs of the bile micelles mixed with MSM/cholesterol, ESM/cholesterol, and MFGM phospholipid/cholesterol were equal to the control (PIPES buffer + bovine bile), indicating negligible swelling of the biliary mixed micelles.
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18
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Pal VK, Roy S. Cooperative Calcium Phosphate Deposition on Collagen-Inspired Short Peptide Nanofibers for Application in Bone Tissue Engineering. Biomacromolecules 2023; 24:807-824. [PMID: 36649490 DOI: 10.1021/acs.biomac.2c01262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In recent years, immense attention has been devoted over the production of osteoinductive materials. To this direction, collagen has a dominant role in developing hard tissues and plays a crucial role in the biomineralization of these tissues. Here, we demonstrated for the first time the potential of the shortest molecular pentapeptide domain inspired from collagen toward mineralizing hydroxyapatite on peptide fibers to develop bone-filling material. Our simplistic approach adapted the easy and facile route of introducing the metal ions onto the peptide nanofibers, displaying adsorbed glutamate onto the surface. This negatively charged surface further induces the nucleation of the crystalline growth of hydroxyapatite. Interestingly, nucleation and growth of the hydroxyapatite crystals lead to the formation of a self-supporting hydrogel to construct a suitable interface for cellular interactions. Furthermore, microscopic and spectroscopic investigations revealed the crystalline growth of the hydroxyapatite onto peptide fibers. The physical properties were also influenced by this crystalline deposition, as evident from the hierarchical organization leading to hydrogels with enhanced mechanical stiffness and improved thermal stability of the scaffold. Furthermore, the mineralized peptide fibers were highly compatible with osteoblast cells and showed increased cellular biomarkers production, which further reinforced the potential application toward effectively fabricating the grafts for bone tissue engineering.
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Affiliation(s)
- Vijay Kumar Pal
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali140306, India
| | - Sangita Roy
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali140306, India
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19
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Byer AS, Pei X, Patterson MG, Ando N. Small-angle X-ray scattering studies of enzymes. Curr Opin Chem Biol 2023; 72:102232. [PMID: 36462455 PMCID: PMC9992928 DOI: 10.1016/j.cbpa.2022.102232] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/14/2022] [Accepted: 10/22/2022] [Indexed: 12/02/2022]
Abstract
Enzyme function requires conformational changes to achieve substrate binding, domain rearrangements, and interactions with partner proteins, but these movements are difficult to observe. Small-angle X-ray scattering (SAXS) is a versatile structural technique that can probe such conformational changes under solution conditions that are physiologically relevant. Although it is generally considered a low-resolution structural technique, when used to study conformational changes as a function of time, ligand binding, or protein interactions, SAXS can provide rich insight into enzyme behavior, including subtle domain movements. In this perspective, we highlight recent uses of SAXS to probe structural enzyme changes upon ligand and partner-protein binding and discuss tools for signal deconvolution of complex protein solutions.
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Affiliation(s)
- Amanda S Byer
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Xiaokun Pei
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael G Patterson
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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20
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Fandrich P, Esteban Vázquez J, Haverkamp R, Hellweg T. Growth of Smart Microgels in a Flow Reactor Scrutinized by In-Line SAXS. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1084-1092. [PMID: 36630721 DOI: 10.1021/acs.langmuir.2c02796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In this work, a continuous flow setup for in situ investigation of microgel growth with small-angle X-ray scattering (SAXS) is established. Poly(N-n-propylacrylamide) (PNNPAM) and poly(N-isopropylacrylamide) (PNIPAM) microgels are synthesized in H2O at different residence times inside a continuous flow reactor. The microgels are investigated by in situ SAXS and ex situ photon correlation spectroscopy. The size of the microgels was found to be reproducible in independent experiments with run times of up to 7 h. Already the scattering curves of the microgels with a time of residence of 15 min show a well-defined form factor. Further analysis of the scattering profiles confirms the spherical shape of the microgels. At a residence time of 2 min, the scattering intensity is significantly lower corresponding to a smaller particle size. The experimental conditions remain constant over time, which is crucial for long-time experiments. The PNNPAM system is found to be more suitable for the flow reactor experiment with in-line SAXS as it shows less polymer deposition in the tubing and forms particles with lower polydispersity. The presented reactor is characterized by a compact design and offers a plug-and-play setup close to the sample environment. This work paves the way for investigations of microgel growth at e.g. synchrotron X-ray beamlines.
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Affiliation(s)
- Pascal Fandrich
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615Bielefeld, Germany
| | - Jorge Esteban Vázquez
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615Bielefeld, Germany
| | - René Haverkamp
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615Bielefeld, Germany
| | - Thomas Hellweg
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615Bielefeld, Germany
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21
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Byrnes J, Chopra K, Rolband LA, Danai L, Chodankar S, Yang L, Afonin KA. Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD. Methods Mol Biol 2023; 2709:65-94. [PMID: 37572273 PMCID: PMC10484297 DOI: 10.1007/978-1-0716-3417-2_4] [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] [Indexed: 08/14/2023]
Abstract
Structural characterization of nucleic acid nanoparticles (NANPs) in solution is critical for validation of correct assembly and for quantifying the size, shape, and flexibility of the construct. Small-angle X-ray scattering (SAXS) is a well-established method to obtain structural information of particles in solution. Here, we present a procedure for the preparation of NANPs for SAXS. This procedure outlines the steps for a successful SAXS experiment and the use of SAXS-driven molecular dynamics to generate an ensemble of structures that best explain the data observed in solution. We use an RNA NANP as an example, so the reader can prepare the sample for data collection, analyze the results, and perform SAXS-driven MD on similar NANPs.
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Affiliation(s)
| | | | - Lewis A Rolband
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Leyla Danai
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | - Lin Yang
- Brookhaven National Laboratory, Upton, NY, USA
| | - Kirill A Afonin
- University of North Carolina at Charlotte, Charlotte, NC, USA
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22
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Myatt DP, Wharram L, Graham C, Liddell J, Branton H, Pizzey C, Cowieson N, Rambo R, Shattock RJ. Biophysical characterization of the structure of a SARS-CoV-2 self-amplifying RNA (saRNA) vaccine. Biol Methods Protoc 2023; 8:bpad001. [PMID: 36915370 PMCID: PMC10008065 DOI: 10.1093/biomethods/bpad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/13/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
The current SARS-Covid-2 (SARS-CoV-2) pandemic has led to an acceleration of messenger ribonucleic acid (mRNA) vaccine technology. The development of production processes for these large mRNA molecules, especially self-amplifying mRNA (saRNA), has required concomitant development of analytical characterization techniques. Characterizing the purity, shape and structure of these biomolecules is key to their successful performance as drug products. This article describes the biophysical characterization of the Imperial College London Self-amplifying viral RNA vaccine (IMP-1) developed for SARS-CoV-2. A variety of analytical techniques have been used to characterize the IMP-1 RNA molecule. In this article, we use ultraviolet spectroscopy, dynamic light scattering, size-exclusion chromatography small-angle X-ray scattering and circular dichroism to determine key biophysical attributes of IMP-1. Each technique provides important information about the concentration, size, shape, structure and purity of the molecule.
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Affiliation(s)
- Daniel P Myatt
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - Lewis Wharram
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - Charlotte Graham
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - John Liddell
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - Harvey Branton
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - Claire Pizzey
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Nathan Cowieson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Robert Rambo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Robin J Shattock
- Department of Infectious Disease, Imperial College London, London W21PG, UK
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23
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Ashish. Visualizing how inclusion of higher reciprocal space in SWAXS data analysis improves shape restoration of biomolecules: case of lysozyme. J Biomol Struct Dyn 2022; 40:12975-12989. [PMID: 34569414 DOI: 10.1080/07391102.2021.1977704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Query remains whether use of increased resolution data from X-ray scattering aids in better understanding of the dynamic shape of the biomolecule in solution? To address this, we acquired Small/Wide angle X-ray scattering (SWAXS) data in the q range of 0.008 - 1.72 Å-1 from dilute solutions of lysozyme (0.9 to 5 mg/ml). Samples lacked any interparticulate effect and datasets showed Bragg peaks at q∼0.325, 0.65 and 1.4 Å-1, as reported before by other authors. Considering an averaged profile, we estimated shape parameters and distance distribution profiles of interatomic vectors by gradually increasing input qmax value. Interestingly, use of higher resolution led to emergence of new peaks amongst smaller vectors. Deconvolution of these peaks provided positions of smaller peaks which correlated well with an earlier theoretical work. These peaks arise from secondary structures or due to non-uniform internal motions within the larger shape of this protein. Dummy residue modeling considering uniform density yielded model(s) with holes or cavities when considering higher q values implying limitations of this method. Employing normal mode calculations, we searched for better fitting model of lysozyme using differentially ranged SWAXS data and a crystal structure of lysozyme as starting structure. Comparison of refined models with structures from crystallography and NMR data showed that use of data till mid q region resulted in adjustments near the center of mass of starting structure, and inclusion of higher resolution induced pan-structure adjustments. We conclude that high resolution SWAXS data analysis provides additional dimension towards understanding biomolecular structural dynamics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashish
- CSIR-Institute of Microbial Technology, Chandigarh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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24
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Gama Lima Costa R, Fushman D. Reweighting methods for elucidation of conformation ensembles of proteins. Curr Opin Struct Biol 2022; 77:102470. [PMID: 36183447 PMCID: PMC9771963 DOI: 10.1016/j.sbi.2022.102470] [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: 06/10/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/24/2022]
Abstract
Proteins are inherently dynamic macromolecules that exist in equilibrium among multiple conformational states, and motions of protein backbone and side chains are fundamental to biological function. The ability to characterize the conformational landscape is particularly important for intrinsically disordered proteins, multidomain proteins, and weakly bound complexes, where single-structure representations are inadequate. As the focus of structural biology shifts from relatively rigid macromolecules toward larger and more complex systems and molecular assemblies, there is a need for structural approaches that can paint a more realistic picture of such conformationally heterogeneous systems. Here, we review reweighting methods for elucidation of structural ensembles based on experimental data, with the focus on applications to multidomain proteins.
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Affiliation(s)
- Raquel Gama Lima Costa
- Chemical Physics Program, Institute for Physical Sciences and Technology, University of Maryland, College Park, 20742, MD, USA.
| | - David Fushman
- Chemical Physics Program, Institute for Physical Sciences and Technology, University of Maryland, College Park, 20742, MD, USA; Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, 20742, MD, USA.
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25
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Barnsley LC, Nandakumaran N, Feoktystov A, Dulle M, Fruhner L, Feygenson M. A reverse Monte Carlo algorithm to simulate two-dimensional small-angle scattering intensities. J Appl Crystallogr 2022; 55:1592-1602. [PMID: 36570657 PMCID: PMC9721324 DOI: 10.1107/s1600576722009219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Small-angle scattering (SAS) experiments are a powerful method for studying self-assembly phenomena in nanoscopic materials because of the sensitivity of the technique to structures formed by interactions on the nanoscale. Numerous out-of-the-box options exist for analysing structures measured by SAS but many of these are underpinned by assumptions about the underlying interactions that are not always relevant for a given system. Here, a numerical algorithm based on reverse Monte Carlo simulations is described to model the intensity observed on a SAS detector as a function of the scattering vector. The model simulates a two-dimensional detector image, accounting for magnetic scattering, instrument resolution, particle polydispersity and particle collisions, while making no further assumptions about the underlying particle interactions. By simulating a two-dimensional image that can be potentially anisotropic, the algorithm is particularly useful for studying systems driven by anisotropic interactions. The final output of the algorithm is a relative particle distribution, allowing visualization of particle structures that form over long-range length scales (i.e. several hundred nanometres), along with an orientational distribution of magnetic moments. The effectiveness of the algorithm is shown by modelling a SAS experimental data set studying finite-length chains consisting of magnetic nanoparticles, which assembled in the presence of a strong magnetic field due to dipole interactions.
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Affiliation(s)
- Lester C. Barnsley
- Australian Synchrotron, ANSTO, Clayton 3168, Australia,Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), 85748 Garching, Germany,Correspondence e-mail:
| | - Nileena Nandakumaran
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS-2) and Peter Grünberg Institut (PGI), JARA-FIT, 52425 Jülich, Germany,Lehrstuhl für Experimentalphysik IVc, RWTH Aachen University, 52056 Aachen, Germany
| | - Artem Feoktystov
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), 85748 Garching, Germany
| | - Martin Dulle
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS-1), 52425 Jülich, Germany
| | - Lisa Fruhner
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS-1), 52425 Jülich, Germany
| | - Mikhail Feygenson
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS-1), 52425 Jülich, Germany,European Spallation Source ERIC, SE-22100 Lund, Sweden
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26
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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27
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Wojciechowska D, Taube M, Rucińska K, Maksim J, Kozak M. Oligomerization of Human Cystatin C—An Amyloidogenic Protein: An Analysis of Small Oligomeric Subspecies. Int J Mol Sci 2022; 23:ijms232113441. [PMID: 36362228 PMCID: PMC9656228 DOI: 10.3390/ijms232113441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Human cystatin C (HCC), an amyloidogenic protein, forms dimers and higher oligomers (trimers, tetramers and donut like large oligomers) via a domain-swapping mechanism. The aim of this study was the characterization of the HCC oligomeric states observed within the pH range from 2.2 to 10.0 and also in conditions promoting oligomerization. The HCC oligomeric forms obtained in different conditions were characterized using size exclusion chromatography, dynamic light scattering and small-angle X-ray scattering. The marked ability of HCC to form tetramers at low pH (2.3 or 3.0) and dimers at pH 4.0–5.0 was observed. HCC remains monomeric at pH levels above 6.0. Based on the SAXS data, the structure of the HCC tetramer was proposed. Changes in the environment (from acid to neutral) induced a breakdown of the HCC tetramers to dimers. The tetrameric forms of human cystatin C are formed by the association of the dimers without a domain-swapping mechanism. These observations were confirmed by their dissociation to dimers at pH 7.4.
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Affiliation(s)
- Daria Wojciechowska
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Michał Taube
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Karolina Rucińska
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Joanna Maksim
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, 30-392 Kraków, Poland
- Correspondence:
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28
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Trewhella J, Vachette P, Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland TE, Cowieson N, Crossett B, Duff AP, Franke D, Gabel F, Gillilan RE, Graewert M, Grishaev A, Guss JM, Hammel M, Hopkins J, Huang Q, Hub JS, Hura GL, Irving TC, Jeffries CM, Jeong C, Kirby N, Krueger S, Martel A, Matsui T, Li N, Pérez J, Porcar L, Prangé T, Rajkovic I, Rocco M, Rosenberg DJ, Ryan TM, Seifert S, Sekiguchi H, Svergun D, Teixeira S, Thureau A, Weiss TM, Whitten AE, Wood K, Zuo X. A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking. Acta Crystallogr D Struct Biol 2022; 78:1315-1336. [PMID: 36322416 PMCID: PMC9629491 DOI: 10.1107/s2059798322009184] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022] Open
Abstract
Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0-1 Å-1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to <0.5 Å-1, but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H2O and in D2O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å-1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Patrice Vachette
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Paris, 91198 Gif-sur-Yvette, France
| | - Jan Bierma
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Clement Blanchet
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Emre Brookes
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Srinivas Chakravarthy
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Leonie Chatzimagas
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123 Saarbrücken, Germany
| | - Thomas E. Cleveland
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Nathan Cowieson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Ben Crossett
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Daniel Franke
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Frank Gabel
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoblé Alpes, 41 Rue Jules Horowitz, 38027 Grenoble, France
| | - Richard E. Gillilan
- Cornell High-Energy Synchrotron Source, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Melissa Graewert
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jesse Hopkins
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Qingqui Huang
- Cornell High-Energy Synchrotron Source, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123 Saarbrücken, Germany
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas C. Irving
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Cy Michael Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Cheol Jeong
- Department of Physics, Wesleyan University, Middletown, CT 06459, USA
| | - Nigel Kirby
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3158, Australia
| | - Susan Krueger
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Anne Martel
- Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9, France
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Na Li
- National Facility for Protein Science in Shanghai, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Road No. 333, Haike Road, Shanghai 201210, People’s Republic of China
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette, France
| | - Lionel Porcar
- Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9, France
| | - Thierry Prangé
- CITCoM (UMR 8038 CNRS), Faculté de Pharmacie, 4 Avenue de l’Observatoire, 75006 Paris, France
| | - Ivan Rajkovic
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mattia Rocco
- Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132 Genova, Italy
| | - Daniel J. Rosenberg
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Timothy M. Ryan
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3158, Australia
| | - Soenke Seifert
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Hiroshi Sekiguchi
- SPring-8, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyōgo 679-5198, Japan
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Susana Teixeira
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
| | - Aurelien Thureau
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette, France
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Xiaobing Zuo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
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29
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Whitten AE, Jeffries CM. Data analysis and modeling of small-angle neutron scattering data with contrast variation from bio-macromolecular complexes. Methods Enzymol 2022; 678:55-96. [PMID: 36641217 DOI: 10.1016/bs.mie.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Small-angle neutron scattering (SANS) with contrast variation (CV) is a valuable technique in the structural biology toolchest. Accurate structural parameters-e.g., radii of gyration, volumes, dimensions, and distance distribution(s)-can be derived from the SANS-CV data to yield the shape and disposition of the individual components within stable complexes. Contrast variation is achieved through the substitution of hydrogen isotopes (1H for 2H) in molecules and solvents to alter the neutron scattering properties of each component of a complex. While SANS-CV can be used a stand-alone technique for interrogating the overall structure of biomacromolecules in solution, it also complements other methods such as small-angle X-ray scattering, crystallography, nuclear magnetic resonance, and cryo-electron microscopy. Undertaking a SANS-CV experiment is challenging, due in part to the preparation of significant quantities of monodisperse samples that may require deuterium (2H) labeling. Nevertheless, SANS-CV can be used to study a diverse range biomacromolecular complexes including protein-protein and protein-nucleic acid systems, membrane proteins, and flexible systems resistant to crystallization. This chapter describes how to approach the data analysis and modeling of SANS data, including: (1) Analysis of the forward scattering (I(0)) and calculation of theoretical estimates of contrast; (2) Analysis of the contrast dependence of the radius of gyration using the Stuhrmann plot and parallel axis theorem; (3) Calculation of composite scattering functions to evaluate the size, shape, and dispositions of individual components within a complex, and; (4) Development of real-space models to fit the SANS-CV data using volume-element bead modeling or atomistic rigid body modeling.
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Affiliation(s)
- Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia.
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, c/o Deutsches Elektronen-Synchrotron, Hamburg, Germany.
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30
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San Emeterio J, Pabit SA, Pollack L. Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis. Methods Enzymol 2022; 677:41-83. [PMID: 36410957 PMCID: PMC10015503 DOI: 10.1016/bs.mie.2022.08.007] [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] [Indexed: 11/19/2022]
Abstract
Proteins and nucleic acids, alone and in complex are among the essential building blocks of living organisms. Obtaining a molecular level understanding of their structures, and the changes that occur as they interact, is critical for expanding our knowledge of life processes or disease progression. Here, we motivate and describe an application of solution small angle X-ray scattering (SAXS) which provides valuable information about the structures, ensembles, compositions and dynamics of protein-nucleic acid complexes in solution, in equilibrium and time-resolved studies. Contrast variation (CV-) SAXS permits the visualization of the distinct molecular constituents (protein and/or nucleic acid) within a complex. CV-SAXS can be implemented in two modes. In the simplest, the protein within the complex is effectively rendered invisible by the addition of an inert contrast agent at an appropriate concentration. Under these conditions, the structure, or structural changes of only the nucleic acid component of the complex can be studied in detail. The second mode permits observation of both components of the complex: the protein and the nucleic acid. This approach requires the acquisition of SAXS profiles on the complex at different concentrations of a contrast agent. Here, we review CV-SAXS as applied to protein-nucleic acid complexes in both modes. We provide some theoretical framework for CV-SAXS but focus primarily on providing the necessary information required to implement a successful experiment including experimental design, sample quality assessment, and data analysis.
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Affiliation(s)
- Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States.
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31
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Cheung E, Xia Y, Caporini MA, Gilmore JL. Tools shaping drug discovery and development. BIOPHYSICS REVIEWS 2022; 3:031301. [PMID: 38505278 PMCID: PMC10903431 DOI: 10.1063/5.0087583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/21/2022] [Indexed: 03/21/2024]
Abstract
Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.
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Affiliation(s)
- Eugene Cheung
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Yan Xia
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Marc A. Caporini
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jamie L. Gilmore
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
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32
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Andrusenko I, Gemmi M. 3D
electron diffraction for structure determination of small‐molecule nanocrystals: A possible breakthrough for the pharmaceutical industry. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1810. [PMID: 35595285 PMCID: PMC9539612 DOI: 10.1002/wnan.1810] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Iryna Andrusenko
- Center for Materials Interfaces, Electron Crystallography Istituto Italiano di Tecnologia Pontedera
| | - Mauro Gemmi
- Center for Materials Interfaces, Electron Crystallography Istituto Italiano di Tecnologia Pontedera
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33
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Otto F, Sun X, Schulz F, Sanchez-Cano C, Feliu N, Westermeier F, Parak WJ. X-Ray Photon Correlation Spectroscopy Towards Measuring Nanoparticle Diameters in Biological Environments Allowing for the In Situ Analysis of their Bio-Nano Interface. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201324. [PMID: 35905490 DOI: 10.1002/smll.202201324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/06/2022] [Indexed: 06/15/2023]
Abstract
X-ray photon correlation spectroscopy (XPCS), a synchrotron source-based technique to measure sample dynamics, is used to determine hydrodynamic diameters of gold nanoparticles (Au NPs) of different sizes in biological environments. In situ determined hydrodynamic diameters are benchmarked with values obtained by dynamic light scattering. The technique is then applied to analyze the behavior of the Au NPs in a biological environment. First, a concentration-dependent agglomeration in the presence of NaCl is determined. Second, concentration-dependent increase in hydrodynamic diameter of the Au NPs upon the presence of proteins is determined. As X-rays in the used energy range are barely scattered by biological matter, dynamics of the Au NPs can be also detected in situ in complex biological environments, such as blood. These measurements demonstrate the possibility of XPCS for in situ analytics of nanoparticles (NPs) in biological environments where similar detection techniques based on visible light would severely suffer from scattering, absorption, and reflection effects.
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Affiliation(s)
- Ferdinand Otto
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Xing Sun
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Hunan University, Lushan Road (S) 2, Changsha, 410012, P. R. China
| | - Florian Schulz
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Carlos Sanchez-Cano
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia-San Sebastian, 20018, Spain
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, Bilbao, 48009, Spain
| | - Neus Feliu
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Fraunhofer Center for Applied Nanotechnology (IAP-CAN), Grindelallee 117, 20146, Hamburg, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany
| | - Wolfgang J Parak
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
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34
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Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, Wan Y, Wang Z, Xue Y, Zhang H, Zhang QC, Zhou Y. Recent advances in RNA structurome. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1285-1324. [PMID: 35717434 PMCID: PMC9206424 DOI: 10.1007/s11427-021-2116-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangnan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siwy Ling Yang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jieyu Zhao
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chun Kit Kwok
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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35
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Krueger S. Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs. Curr Opin Struct Biol 2022; 74:102375. [PMID: 35490650 PMCID: PMC10988784 DOI: 10.1016/j.sbi.2022.102375] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/09/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
Small-angle neutron scattering (SANS) has been a beneficial tool for studying the structure of biological macromolecules in solution for several decades. Continued improvements in sample preparation techniques, including deuterium labeling, neutron instrumentation and complementary techniques such as small-angle x-ray scattering (SAXS), cryo-EM, NMR and x-ray crystallography, along with the availability of more powerful structure prediction algorithms and computational resources has made SANS more important than ever as a means to obtain unique information on the structure of biological complexes in solution. In particular, the contrast variation (CV) technique, which requires a large commitment in both sample preparation and measurement time, has become more practical with the advent of these improved resources. Here, challenges and recent triumphs as well as future prospects are discussed.
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Affiliation(s)
- Susan Krueger
- NIST Center for Neutron Research, NIST, Gaithersburg, MD, 20899, USA.
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36
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Xu X, Sun J, Bing L, Cui X, Jia B, Bai S. Fractal features of dual temperature/pH-sensitive poly(N-isopropylacrylamide-co-acrylic acid) hydrogels and resultant effects on the controlled drug delivery performances. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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37
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Watchorn J, Clasky AJ, Prakash G, Johnston IAE, Chen PZ, Gu FX. Untangling Mucosal Drug Delivery: Engineering, Designing, and Testing Nanoparticles to Overcome the Mucus Barrier. ACS Biomater Sci Eng 2022; 8:1396-1426. [PMID: 35294187 DOI: 10.1021/acsbiomaterials.2c00047] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mucus is a complex viscoelastic gel and acts as a barrier covering much of the soft tissue in the human body. High vascularization and accessibility have motivated drug delivery to various mucosal surfaces; however, these benefits are hindered by the mucus layer. To overcome the mucus barrier, many nanomedicines have been developed, with the goal of improving the efficacy and bioavailability of drug payloads. Two major nanoparticle-based strategies have emerged to facilitate mucosal drug delivery, namely, mucoadhesion and mucopenetration. Generally, mucoadhesive nanoparticles promote interactions with mucus for immobilization and sustained drug release, whereas mucopenetrating nanoparticles diffuse through the mucus and enhance drug uptake. The choice of strategy depends on many factors pertaining to the structural and compositional characteristics of the target mucus and mucosa. While there have been promising results in preclinical studies, mucus-nanoparticle interactions remain poorly understood, thus limiting effective clinical translation. This article reviews nanomedicines designed with mucoadhesive or mucopenetrating properties for mucosal delivery, explores the influence of site-dependent physiological variation among mucosal surfaces on efficacy, transport, and bioavailability, and discusses the techniques and models used to investigate mucus-nanoparticle interactions. The effects of non-homeostatic perturbations on protein corona formation, mucus composition, and nanoparticle performance are discussed in the context of mucosal delivery. The complexity of the mucosal barrier necessitates consideration of the interplay between nanoparticle design, tissue-specific differences in mucus structure and composition, and homeostatic or disease-related changes to the mucus barrier to develop effective nanomedicines for mucosal delivery.
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Affiliation(s)
- Jeffrey Watchorn
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Aaron J Clasky
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Gayatri Prakash
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Ian A E Johnston
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Paul Z Chen
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Frank X Gu
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada.,Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
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38
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Golub M, Gätcke J, Subramanian S, Kölsch A, Darwish T, Howard JK, Feoktystov A, Matsarskaia O, Martel A, Porcar L, Zouni A, Pieper J. "Invisible" Detergents Enable a Reliable Determination of Solution Structures of Native Photosystems by Small-Angle Neutron Scattering. J Phys Chem B 2022; 126:2824-2833. [PMID: 35384657 DOI: 10.1021/acs.jpcb.2c01591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photosystems I (PSI) and II (PSII) are pigment-protein complexes capable of performing the light-induced charge separation necessary to convert solar energy into a biochemically storable form, an essential step in photosynthesis. Small-angle neutron scattering (SANS) is unique in providing structural information on PSI and PSII in solution under nearly physiological conditions without the need for crystallization or temperature decrease. We show that the reliability of the solution structure critically depends on proper contrast matching of the detergent belt surrounding the protein. Especially, specifically deuterated ("invisible") detergents are shown to be properly matched out in SANS experiments by a direct, quantitative comparison with conventional matching strategies. In contrast, protonated detergents necessarily exhibit incomplete matching so that related SANS results systematically overestimate the size of the membrane protein under study. While the solution structures obtained are close to corresponding high-resolution structures, we show that temperature and solution state lead to individual structural differences compared with high-resolution structures. We attribute these differences to the presence of a manifold of conformational substates accessible by protein dynamics under physiological conditions.
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Affiliation(s)
- M Golub
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | - J Gätcke
- Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - S Subramanian
- Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - A Kölsch
- Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - T Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - J K Howard
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - A Feoktystov
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748 Garching, Germany
| | - O Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs CS 20156, 38042 Grenoble Cedex 9, France
| | - A Martel
- Institut Laue-Langevin, 71 Avenue des Martyrs CS 20156, 38042 Grenoble Cedex 9, France
| | - L Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs CS 20156, 38042 Grenoble Cedex 9, France
| | - A Zouni
- Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - J Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
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39
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Golub M, Lokstein H, Soloviov D, Kuklin A, Wieland DCF, Pieper J. Light-Harvesting Complex II Adopts Different Quaternary Structures in Solution as Observed Using Small-Angle Scattering. J Phys Chem Lett 2022; 13:1258-1265. [PMID: 35089716 DOI: 10.1021/acs.jpclett.1c03614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The high-resolution crystal structure of the trimeric major light-harvesting complex of photosystem II (LHCII) is often perceived as the basis for understanding its light-harvesting and photoprotective functions. However, the LHCII solution structure and its oligomerization or aggregation state may generally differ from the crystal structure and, moreover, also depend on its functional state. In this regard, small-angle scattering experiments provide the missing link by offering structural information in aqueous solution at physiological temperatures. Herein, we use small-angle scattering to investigate the solution structures of two different preparations of solubilized LHCII employing the nonionic detergents n-octyl-β-d-glucoside (OG) and n-dodecyl-β-D-maltoside (β-DM). The data reveal that the LHCII-OG complex is equivalent to the trimeric crystal structure. Remarkably, however, we observe─for the first time─a stable oligomer composed of three LHCII trimers in the case of the LHCII-β-DM preparation, implying additional pigment-pigment interactions. The latter complex is assumed to mimic trimer-trimer interactions which play an important role in the context of photoprotective nonphotochemical quenching.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 121 16 Prague, Czech Republic
| | - Dmytro Soloviov
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia
- Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
- Institute for Safety Problems of Nuclear Power Plants NAS of Ukraine, Lysogirska str. 12, 03028 Kyiv, Ukraine
| | - Alexander Kuklin
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia
- Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - D C Florian Wieland
- Helmholtz Zentrum Geesthacht, Institute for Materials Research, Department for Metallic Biomaterials, 21502 Geesthacht, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald str. 1, 50411 Tartu, Estonia
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40
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Martel A, Gabel F. Time-resolved small-angle neutron scattering (TR-SANS) for structural biology of dynamic systems: Principles, recent developments, and practical guidelines. Methods Enzymol 2022; 677:263-290. [DOI: 10.1016/bs.mie.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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41
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Sagar A, Bernadó P. Disentangling polydisperse biomolecular systems by Chemometrics decomposition of SAS data. Methods Enzymol 2022; 677:531-555. [DOI: 10.1016/bs.mie.2022.08.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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42
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Krueger S. Planning, executing and assessing the validity of SANS contrast variation experiments. Methods Enzymol 2022; 677:127-155. [DOI: 10.1016/bs.mie.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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43
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Graewert MA, Svergun DI. Advanced sample environments and sample requirements for biological SAXS. Methods Enzymol 2022; 677:1-39. [DOI: 10.1016/bs.mie.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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44
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Gillilan RE. High-pressure SAXS, deep life, and extreme biophysics. Methods Enzymol 2022; 677:323-355. [DOI: 10.1016/bs.mie.2022.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Pietras Z, Wood K, Whitten AE, Jeffries CM. Technical considerations for small-angle neutron scattering from biological macromolecules in solution: Cross sections, contrasts, instrument setup and measurement. Methods Enzymol 2022; 677:157-189. [DOI: 10.1016/bs.mie.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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46
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Matsuo T, Peters J. Fiber Diffraction and Small-Angle Scattering for Structural Investigation of Bacterial Amyloids. Methods Mol Biol 2022; 2538:95-107. [PMID: 35951295 DOI: 10.1007/978-1-0716-2529-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
X-ray/neutron fiber diffraction and small-angle X-ray/neutron scattering are widely used to investigate the molecular structure of fibrous proteins, including amyloid fibrils. However, there is sometimes confusion between these two techniques despite the fact that sample conditions and the content of the information obtained are not the same. In this brief chapter, we present the differences in sample conditions between these two methods, and their effects on experimentally obtained diffraction or scattering patterns, emphasizing the degree of disorder in the samples.
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Affiliation(s)
- Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France.
- Institut Laue-Langevin, Grenoble Cedex 9, France.
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki, Japan.
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France.
- Institut Laue-Langevin, Grenoble Cedex 9, France.
- Institut Universitaire de France, Paris, France.
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47
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Zhang F, Richter G, Bourgeois B, Spreitzer E, Moser A, Keilbach A, Kotnik P, Madl T. A General Small-Angle X-ray Scattering-Based Screening Protocol for Studying Physical Stability of Protein Formulations. Pharmaceutics 2021; 14:69. [PMID: 35056965 PMCID: PMC8778066 DOI: 10.3390/pharmaceutics14010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
A fundamental step in developing a protein drug is the selection of a stable storage formulation that ensures efficacy of the drug and inhibits physiochemical degradation or aggregation. Here, we designed and evaluated a general workflow for screening of protein formulations based on small-angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling, temperature control, and fast data analysis and provides protein particle interaction information. SAXS, together with different methods including turbidity analysis, dynamic light scattering (DLS), and SDS-PAGE measurements, were used to obtain different parameters to provide high throughput screenings. Using a set of model proteins and biopharmaceuticals, we show that SAXS is complementary to dynamic light scattering (DLS), which is widely used in biopharmaceutical research and industry. We found that, compared to DLS, SAXS can provide a more sensitive measure for protein particle interactions, such as protein aggregation and repulsion. Moreover, we show that SAXS is compatible with a broader range of buffers, excipients, and protein concentrations and that in situ SAXS provides a sensitive measure for long-term protein stability. This workflow can enable future high-throughput analysis of proteins and biopharmaceuticals and can be integrated with well-established complementary physicochemical analysis pipelines in (biopharmaceutical) research and industry.
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Affiliation(s)
- Fangrong Zhang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China;
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Gesa Richter
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Armin Moser
- Anton Paar GmbH, 8054 Graz, Austria; (A.M.); (A.K.); (P.K.)
| | | | - Petra Kotnik
- Anton Paar GmbH, 8054 Graz, Austria; (A.M.); (A.K.); (P.K.)
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
- BioTechMed-Graz, 8010 Graz, Austria
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48
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Geue N, Winpenny REP, Barran PE. Structural characterisation methods for supramolecular chemistry that go beyond crystallography. Chem Soc Rev 2021; 51:8-27. [PMID: 34817479 DOI: 10.1039/d0cs01550d] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Supramolecular chemistry has grown rapidly over the past three decades, yet synthetic supramolecular chemists still face several challenges when it comes to characterising their compounds. In this review, we present an introduction to structural characterisation techniques commonly used for non-crystalline supramolecular molecules, e.g. nuclear magnetic and electron paramagnetic resonance spectroscopy (NMR and EPR), mass spectrometry (MS), ion mobility mass spectrometry (IM-MS), small-angle neutron and X-ray scattering (SANS and SAXS) as well as cryogenic transmission electron microscopy (cryo-TEM). We provide an overview of their fundamental concepts based on case studies from different fields of supramolecular chemistry, e.g. interlocked structures, molecular self-assembly and host-guest chemistry, while focussing on particular strengths and weaknesses of the discussed methods. Additionally, three multi-technique case studies are examined in detail to illustrate the benefits of using complementary techniques simultaneously.
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Affiliation(s)
- Niklas Geue
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Richard E P Winpenny
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
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49
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Methods for Small-Angle Scattering Measurements on Peptiplexes of DNA with Cell-Penetrating Peptides. Methods Mol Biol 2021. [PMID: 34766290 DOI: 10.1007/978-1-0716-1752-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Peptiplexes are soft biomaterials formed through the noncovalent association between cell-penetrating peptides and nucleic acids. Although internalization often involves electrostatic anchoring followed by endocytosis, the mode of action of these transporters remains elusive in many cases, and proper understanding of mechanisms behind their penetrating capabilities necessarily entails structural data at the nanoscopic scale. In this chapter, we examine the structural landscape of peptiplexes, emphasizing the complex behavior of these polyelectrolyte self-assemblies and how supramolecular order impacts their translocation efficiency. We discuss experimental tools commonly used to investigate the structure of peptiplexes and pay special attention to small-angle X-ray scattering (SAXS) as a suitable method for unveiling their nanoscale organization. A roadmap for standard SAXS measurements in CPP/DNA samples is presented alongside a selection of observations from our own experience dealing with SAXS applied to the investigation of CPPs.
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50
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Sonje J, Thakral S, Krueger S, Suryanarayanan R. Reversible Self-Association in Lactate Dehydrogenase during Freeze-Thaw in Buffered Solutions Using Neutron Scattering. Mol Pharm 2021; 18:4459-4474. [PMID: 34709831 DOI: 10.1021/acs.molpharmaceut.1c00666] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aims of this work were to evaluate the effect of freezing and thawing stresses on lactate dehydrogenase (LDH) stability under three conditions. (i) In a solution buffered with sodium phosphate (NaP; 10 and 100 mM). The selective crystallization of disodium hydrogen phosphate during freezing caused a pronounced pH shift. (ii) In a solution buffered with histidine, where there was no pH shift due to buffer salt crystallization. (iii) At different concentrations of LDH so as to determine the self-stabilizing ability of LDH. The change in LDH tetrameric conformation was measured by small-angle neutron scattering (SANS). The pH of the phosphate buffer solutions was monitored as a function of temperature to quantify the pH shift. The conditions of buffer component crystallization from solution were identified using low-temperature X-ray diffractometry. Dynamic light scattering (DLS) enabled us to determine the effect of freeze-thawing on the protein aggregation behavior. LDH, at a high concentration (1000 μg/mL; buffer concentration 10 mM), has a pronounced self-stabilizing effect and did not aggregate after five freeze-thaw cycles. At lower LDH concentrations (10 and 100 μg/mL), only with the selection of an appropriate buffer, irreversible aggregation could be avoided. While SANS provided qualitative information with respect to protein conformation, the insights from DLS were quantitative with respect to the particle size of the aggregates. SANS is the only technique which can characterize the protein both in the frozen and thawed states.
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Affiliation(s)
- Jayesh Sonje
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, Minnesota 55455, United States
| | - Seema Thakral
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, Minnesota 55455, United States.,Characterization Facility, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Susan Krueger
- Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Raj Suryanarayanan
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, Minnesota 55455, United States
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