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Kozono Y, Kuramochi M, Sasaki YC, Kozono H. Ubiquitination of Major Histocompatibility Complex II Changes Its Immunological Recognition Structure. Int J Mol Sci 2023; 24:17083. [PMID: 38069406 PMCID: PMC10707457 DOI: 10.3390/ijms242317083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Ubiquitination is a process that dictates the lifespan of major histocompatibility complex class II (MHC II)/peptide complexes on antigen-presenting cells. This process is tightly controlled by the levels of ubiquitin ligases, and disruptions in the turnover of MHC II can lead to the improper development of CD4+ T cells within the thymus and hinder the formation of regulatory T cells in the peripheral tissue. To investigate the underlying mechanisms, we utilized dendritic cells lacking the Membrane-associated RING-CH (MARCH) I ubiquitin ligase. We discovered that the overexpression of MARCH I decreases the interaction with LAG-3. Moreover, the MHC II molecules tethered with ubiquitin also showed diminished binding to LAG-3. We employed Diffracted X-ray Blinking (DXB), a technique used for single-molecule X-ray imaging, to observe the protein movements on live cells in real time. Our observations indicated that the normal MHC II molecules moved more rapidly across the cell surface compared to those on the MARCH I-deficient dendritic cells or MHC II KR mutants, which is likely a result of ubiquitination. These findings suggest that the signaling from ubiquitinated MHC II to the T cell receptor differs from the non-ubiquitinated forms. It appears that ubiquitinated MHC II might not be quickly internalized, but rather presents antigens to the T cells, leading to a range of significant immunological responses.
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Affiliation(s)
- Yuko Kozono
- Research Institute for Biomedical Sciences, Tokyo University of Sciences, Noda 278-0022, Chiba, Japan;
| | - Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-0033, Ibaraki, Japan;
| | - Yuji C. Sasaki
- Department of Advanced Material Science, Graduate School for Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Chiba, Japan;
- AIST-U Tokyo Advanced Operando Measurement Technology Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
- Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo 679-5198, Hyogo, Japan
| | - Haruo Kozono
- Research Institute for Biomedical Sciences, Tokyo University of Sciences, Noda 278-0022, Chiba, Japan;
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2
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Lin Y, Sakuraba S, Massilamany C, Reddy J, Tanaka Y, Miyake S, Yamamura T. Harnessing autoimmunity with dominant self-peptide: Modulating the sustainability of tissue-preferential antigen-specific Tregs by governing the binding stability via peptide flanking residues. J Autoimmun 2023; 140:103094. [PMID: 37716077 DOI: 10.1016/j.jaut.2023.103094] [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: 05/25/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 09/18/2023]
Abstract
Sensitization to self-peptides induces various immunological responses, from autoimmunity to tumor immunity, depending on the peptide sequence; however, the underlying mechanisms remain unclear, and thus, curative therapeutic options considering immunity balance are limited. Herein, two overlapping dominant peptides of myelin proteolipid protein, PLP136-150 and PLP139-151, which induce different forms of experimental autoimmune encephalomyelitis (EAE), monophasic and relapsing EAE, respectively, were investigated. Mice with monophasic EAE exhibited highly resistant to EAE re-induction with any encephalitogenic peptides, whereas mice with relapsing EAE were susceptible, and progressed, to EAE re-induction. This resistance to relapse and re-induction in monophasic EAE mice was associated with the maintenance of potent CD69+CD103+CD4+CD25high regulatory T-cells (Tregs) enriched with antigen specificity, which expanded preferentially in the central nervous system with sustained suppressive activity. This tissue-preferential sustainability of potent antigen-specific Tregs was correlated with the antigenicity of PLP136-150, depending on its flanking residues. That is, the flanking residues of PLP136-150 enable to form pivotally arranged strong hydrogen bonds that secured its binding stability to MHC-class II. These potent Tregs acting tissue-preferentially were induced only by sensitization of PLP136-150, not by its tolerance induction, independent of EAE development. These findings suggest that, for optimal therapy, "benign autoimmunity" can be critically achieved through inverse vaccination with self-peptides by manipulating their flanking residues.
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Affiliation(s)
- Youwei Lin
- Department of Immunology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan; Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, 187-8551, Japan.
| | - Shun Sakuraba
- National Institutes for Quantum Science and Technology, Institute for Quantum Life Science, Chiba, 263-0024, Japan.
| | | | - Jayagopala Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, Nagasaki, 852-8588, Japan.
| | - Sachiko Miyake
- Department of Immunology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan.
| | - Takashi Yamamura
- Department of Immunology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan.
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Yamane T, Nakayama T, Ekimoto T, Inoue M, Ikezaki K, Sekiguchi H, Kuramochi M, Terao Y, Judai K, Saito M, Ikeguchi M, Sasaki YC. Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study. Int J Mol Sci 2023; 24:15423. [PMID: 37895101 PMCID: PMC10607685 DOI: 10.3390/ijms242015423] [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: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.
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Affiliation(s)
- Tsutomu Yamane
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
- HPC- and AI-Driven Drug Development Platform Division, Riken Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takahiro Nakayama
- Department of Medical Physiology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka 181-8611, Japan; (T.N.); (Y.T.)
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
| | - Masao Inoue
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
| | - Keigo Ikezaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo 679-5198, Japan;
| | - Masahiro Kuramochi
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
| | - Yasuo Terao
- Department of Medical Physiology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka 181-8611, Japan; (T.N.); (Y.T.)
| | - Ken Judai
- Department of Physics, College of Humanities and Sciences, Nihon University, Sakurajosui 3-25-40, Tokyo 156-8550, Japan;
| | - Minoru Saito
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo 156-8550, Japan;
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
- HPC- and AI-Driven Drug Development Platform Division, Riken Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
- Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo 679-5198, Japan;
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
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Sasaki YC. Diffracted X-ray Tracking for Observing the Internal Motions of Individual Protein Molecules and Its Extended Methodologies. Int J Mol Sci 2023; 24:14829. [PMID: 37834277 PMCID: PMC10573657 DOI: 10.3390/ijms241914829] [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: 09/05/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
In 1998, the diffracted X-ray tracking (DXT) method pioneered the attainment of molecular dynamics measurements within individual molecules. This breakthrough revolutionized the field by enabling unprecedented insights into the complex workings of molecular systems. Similar to the single-molecule fluorescence labeling technique used in the visible range, DXT uses a labeling method and a pink beam to closely track the diffraction pattern emitted from the labeled gold nanocrystals. Moreover, by utilizing X-rays with extremely short wavelengths, DXT has achieved unparalleled accuracy and sensitivity, exceeding initial expectations. As a result, this remarkable advance has facilitated the search for internal dynamics within many protein molecules. DXT has recently achieved remarkable success in elucidating the internal dynamics of membrane proteins in living cell membranes. This breakthrough has not only expanded our knowledge of these important biomolecules but also has immense potential to advance our understanding of cellular processes in their native environment.
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Affiliation(s)
- Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan;
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho 679-5198, Japan
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Oda M. Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking. Int J Mol Sci 2023; 24:13717. [PMID: 37762021 PMCID: PMC10531450 DOI: 10.3390/ijms241813717] [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: 08/17/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Although many protein structures have been determined at atomic resolution, the majority of them are static and represent only the most stable or averaged structures in solution. When a protein binds to its ligand, it usually undergoes fluctuation and changes its conformation. One attractive method for obtaining an accurate view of proteins in solution, which is required for applications such as the rational design of proteins and structure-based drug design, is diffracted X-ray tracking (DXT). DXT can detect the protein structural dynamics on a timeline via gold nanocrystals attached to the protein. Here, the structure dynamics of single-chain Fv antibodies, helix bundle-forming de novo designed proteins, and DNA-binding proteins in both ligand-unbound and ligand-bound states were analyzed using the DXT method. The resultant mean square angular displacements (MSD) curves in both the tilting and twisting directions clearly demonstrated that structural fluctuations were suppressed upon ligand binding, and the binding energies determined using the angular diffusion coefficients from the MSD agreed well with the binding thermodynamics determined using isothermal titration calorimetry. In addition, the size of gold nanocrystals is discussed, which is one of the technical concerns of DXT.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
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Kuramochi M, Dong Y, Yang Y, Arai T, Okada R, Shinkai Y, Doi M, Aoyama K, Sekiguchi H, Mio K, Tsuda S, Sasaki YC. Dynamic motions of ice-binding proteins in living Caenorhabditis elegans using diffracted X-ray blinking and tracking. Biochem Biophys Rep 2022; 29:101224. [PMID: 35146137 PMCID: PMC8819013 DOI: 10.1016/j.bbrep.2022.101224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
- Corresponding author. Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan.
| | - Yige Dong
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yue Yang
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Tatsuya Arai
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Rio Okada
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yoichi Shinkai
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Japan
| | - Motomichi Doi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Japan
| | - Kouki Aoyama
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Hiroshi Sekiguchi
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
| | - Sakae Tsuda
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
- Corresponding author. Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan.
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Ahmad MA, Olule LJA, Meetani M, Sheikh FA, Blooshi RA, Panicker NG, Mustafa F, Rizvi TA. Detection of SARS-CoV-2 in COVID-19 Patient Nasal Swab Samples Using Signal Processing. IEEE JOURNAL OF SELECTED TOPICS IN SIGNAL PROCESSING 2022; 16:164-174. [PMID: 35582704 PMCID: PMC9088791 DOI: 10.1109/jstsp.2021.3134073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 10/18/2021] [Accepted: 12/02/2021] [Indexed: 05/31/2023]
Abstract
This work presents an opto-electrical method that measures the viral nucleocapsid protein and anti-N antibody interactions to differentiate between SARS-CoV-2 negative and positive nasal swab samples. Upon light exposure of the patient nasal swab sample mixed with the anti-N antibody, charge transfer (CT) transitions within the altered protein folds are initiated between the charged amino acids side chain moieties and the peptide backbone that play the role of donor and acceptor groups. A Figure of Merit (FOM) was introduced to correlate the relative variations of the samples with and without antibody at two different voltages. Empirically, SARS-CoV-2 in patient nasal swab samples was detected within two minutes, if an extracted FOM threshold of >1 was achieved; otherwise, the sample wasconsidered negative.
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Affiliation(s)
- Mahmoud Al Ahmad
- Department of Electrical EngineeringUAE UniversityAl Ain15551UAE
- Zayed Center for Health Sciences (ZCHS)UAE UniversityAl Ain15551UAE
| | | | | | | | | | - Neena G. Panicker
- Department of Biochemistry & Molecular BiologyCMHS UAE UniversityAl Ain17666UAE
| | - Farah Mustafa
- Department of Biochemistry and Molecular BiologyCMHS UAE UniversityAl Ain17666UAE
- Zayed Center for Health Sciences (ZCHS)UAE UniversityAl Ain15551UAE
| | - Tahir A. Rizvi
- Department of Microbiology and ImmunologyCMHS UAE UniversityAl Ain17666UAE
- Zayed Center for Health Sciences (ZCHS)UAE UniversityAl Ain15551UAE
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8
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Ahmad MA, Mustafa F, Panicker N, Rizvi TA. Optical Detection of SARS-CoV-2 Utilizing Antigen-Antibody Binding Interactions. SENSORS 2021; 21:s21196596. [PMID: 34640920 PMCID: PMC8512587 DOI: 10.3390/s21196596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease (COVID-19) pandemic, is sweeping the world today. This study investigates the optical detection of SARS-CoV-2, utilizing the antigen-antibody binding interactions utilizing a light source from a smart phone and a portable spectrophotometer. The proof-of-concept is shown by detecting soluble preparations of spike protein subunits from SARS-CoV-2, followed by detection of the actual binding potential of the SARS-CoV-2 proteins with their corresponding antigens. The measured binding interactions for RBD and NCP proteins with their corresponding antibodies under different conditions have been measured and analyzed. Based on these observations, a “hump or spike” in light intensity is observed when a specific molecular interaction takes place between two proteins. The optical responses could further be analyzed using the principle component analysis technique to enhance and allows precise detection of the specific target in a multi-protein mixture.
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Affiliation(s)
- Mahmoud Al Ahmad
- Electrical Engineering Department, United Arab Emirates University, Al Ain 15551, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (F.M.); (T.A.R.)
- Correspondence: ; Tel.: +971-37135150
| | - Farah Mustafa
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (F.M.); (T.A.R.)
- Department of Biochemistry, College of Medicine & Health Sciences, Al Ain 20000, United Arab Emirates;
| | - Neena Panicker
- Department of Biochemistry, College of Medicine & Health Sciences, Al Ain 20000, United Arab Emirates;
| | - Tahir A. Rizvi
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (F.M.); (T.A.R.)
- Department of Microbiology and Immunology, College of Medicine & Health Sciences, Al Ain 20000, United Arab Emirates
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9
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Tilting and rotational motions of silver halide crystal with diffracted X-ray blinking. Sci Rep 2021; 11:4097. [PMID: 33674698 PMCID: PMC7935957 DOI: 10.1038/s41598-021-83320-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022] Open
Abstract
The dynamic properties of crystalline materials are important for understanding their local environment or individual single-grain motions. A new time-resolved observation method is required for use in many fields of investigation. Here, we developed in situ diffracted X-ray blinking to monitor high-resolution diffraction patterns from single-crystal grains with a 50 ms time resolution. The diffraction spots of single grains of silver halides and silver moved in the θ and χ directions during the photolysis chemical reaction. The movements of the spots represent tilting and rotational motions. The time trajectory of the diffraction intensity reflecting those motions was analysed by using single-pixel autocorrelation function (sp-ACF). Single-pixel ACF analysis revealed significant differences in the distributions of the ACF decay constants between silver halides, suggesting that the motions of single grains are different between them. The rotational diffusion coefficients for silver halides were estimated to be accurate at the level of approximately 0.1 to 0.3 pm2/s. Furthermore, newly formed silver grains on silver halides correlated with their ACF decay constants. Our high-resolution atomic scale measurement—sp-ACF analysis of diffraction patterns of individual grains—is useful for evaluating physical properties that are broadly applicable in physics, chemistry, and materials science.
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Buckle AM, Borg NA. Integrating Experiment and Theory to Understand TCR-pMHC Dynamics. Front Immunol 2018; 9:2898. [PMID: 30581442 PMCID: PMC6293202 DOI: 10.3389/fimmu.2018.02898] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
The conformational dynamism of proteins is well established. Rather than having a single structure, proteins are more accurately described as a conformational ensemble that exists across a rugged energy landscape, where different conformational sub-states interconvert. The interaction between αβ T cell receptors (TCR) and cognate peptide-MHC (pMHC) is no exception, and is a dynamic process that involves substantial conformational change. This review focuses on technological advances that have begun to establish the role of conformational dynamics and dynamic allostery in TCR recognition of the pMHC and the early stages of signaling. We discuss how the marriage of molecular dynamics (MD) simulations with experimental techniques provides us with new ways to dissect and interpret the process of TCR ligation. Notably, application of simulation techniques lags behind other fields, but is predicted to make substantial contributions. Finally, we highlight integrated approaches that are being used to shed light on some of the key outstanding questions in the early events leading to TCR signaling.
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Affiliation(s)
- Ashley M Buckle
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Natalie A Borg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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11
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Sekiguchi H, Kuramochi M, Ikezaki K, Okamura Y, Yoshimura K, Matsubara K, Chang JW, Ohta N, Kubo T, Mio K, Suzuki Y, Chavas LMG, Sasaki YC. Diffracted X-ray Blinking Tracks Single Protein Motions. Sci Rep 2018; 8:17090. [PMID: 30504916 PMCID: PMC6269541 DOI: 10.1038/s41598-018-35468-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/06/2018] [Indexed: 11/09/2022] Open
Abstract
Single molecule dynamics studies have begun to use quantum probes. Single particle analysis using cryo-transmission electron microscopy has dramatically improved the resolution when studying protein structures and is shifting towards molecular motion observations. X-ray free-electron lasers are also being explored as routes for determining single molecule structures of biological entities. Here, we propose a new X-ray single molecule technology that allows observation of molecular internal motion over long time scales, ranging from milliseconds up to 103 seconds. Our method uses both low-dose monochromatic X-rays and nanocrystal labelling technology. During monochromatic X-ray diffraction experiments, the intensity of X-ray diffraction from moving single nanocrystals appears to blink because of Brownian motion in aqueous solutions. X-ray diffraction spots from moving nanocrystals were observed to cycle in and out of the Bragg condition. Consequently, the internal motions of a protein molecule labelled with nanocrystals could be extracted from the time trajectory using this diffracted X-ray blinking (DXB) approach. Finally, we succeeded in distinguishing the degree of fluctuation motions of an individual acetylcholine-binding protein (AChBP) interacting with acetylcholine (ACh) using a laboratory X-ray source.
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Affiliation(s)
- Hiroshi Sekiguchi
- Research & Utilization Div., Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 567-5198, Japan.
| | - Masahiro Kuramochi
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Keigo Ikezaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yu Okamura
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Kazuki Yoshimura
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Ken Matsubara
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Jae-Won Chang
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Noboru Ohta
- Research & Utilization Div., Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 567-5198, Japan
| | - Tai Kubo
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,JapanAIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Kazuhiro Mio
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,JapanAIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yoshio Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Leonard M G Chavas
- Proxima-I, Synchrotron SOLEIL, L'Orme des Merisiers Saint-Aubin, BP 48 91192, Gif-sur-Yvette Cedex, France
| | - Yuji C Sasaki
- Research & Utilization Div., Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 567-5198, Japan. .,Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan. .,JapanAIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
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12
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X-ray observations of single bio-supramolecular photochirogenesis. Biophys Chem 2018; 242:1-5. [PMID: 30153504 DOI: 10.1016/j.bpc.2018.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 12/22/2022]
Abstract
The binding and photochirogenic behaviour of 2-anthracenecarboxylate (AC) with human serum albumin (HSA) have hitherto been investigated and comprehended as time-averaged statistical events by spectroscopic examinations and product analyses. In this study, we employed a diffracted X-ray tracking (DXT) technique to visualize the single-molecular dynamics of free and AC-loaded HSA (AC:HSA = 0, 1, 5 and 10), as well as the AC-HSA complex under photoirradiation, all of which were tethered to gold nanocrystals and hence traceable in real time by DXT. This enabled us to draw a more dynamic picture of the bio-supramolecular photochirogenesis at a single-molecule resolution, detailing the softening and flexibility enhancement of HSA upon binding of ACs to its inter-subdomain IIA-IIB site and the dynamic extrusion of AC dimers produced upon photoirradiation.
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13
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Serçinoğlu O, Ozbek P. Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles. J Biomol Struct Dyn 2017; 36:724-740. [DOI: 10.1080/07391102.2017.1295884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Institute of Pure and Applied Sciences, Marmara University, Istanbul, Turkey
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Pemra Ozbek
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
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