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Khan MA, Alhakami H, Alhakami W, Shvetsov AV, Ullah I. A Smart Card-Based Two-Factor Mutual Authentication Scheme for Efficient Deployment of an IoT-Based Telecare Medical Information System. Sensors (Basel) 2023; 23:5419. [PMID: 37420585 DOI: 10.3390/s23125419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 07/09/2023]
Abstract
The integration of the Internet of Things (IoT) and the telecare medical information system (TMIS) enables patients to receive timely and convenient healthcare services regardless of their location or time zone. Since the Internet serves as the key hub for connection and data sharing, its open nature presents security and privacy concerns and should be considered when integrating this technology into the current global healthcare system. Cybercriminals target the TMIS because it holds a lot of sensitive patient data, including medical records, personal information, and financial information. As a result, when developing a trustworthy TMIS, strict security procedures are required to deal with these concerns. Several researchers have proposed smart card-based mutual authentication methods to prevent such security attacks, indicating that this will be the preferred method for TMIS security with the IoT. In the existing literature, such methods are typically developed using computationally expensive procedures, such as bilinear pairing, elliptic curve operations, etc., which are unsuitable for biomedical devices with limited resources. Using the concept of hyperelliptic curve cryptography (HECC), we propose a new solution: a smart card-based two-factor mutual authentication scheme. In this new scheme, HECC's finest properties, such as compact parameters and key sizes, are utilized to enhance the real-time performance of an IoT-based TMIS system. The results of a security analysis indicate that the newly contributed scheme is resistant to a wide variety of cryptographic attacks. A comparison of computation and communication costs demonstrates that the proposed scheme is more cost-effective than existing schemes.
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Affiliation(s)
- Muhammad Asghar Khan
- Department of Electrical Engineering, Hamdard Institute of Engineering and Technology, Hamdard University, Islamabad 44000, Pakistan
| | - Hosam Alhakami
- Department of Computer Science, College of Computer and Information Systems, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Wajdi Alhakami
- Department of Information Technology, College of Computers and Information Technology, Taif University, Taif 21431, Saudi Arabia
| | - Alexey V Shvetsov
- Department of Smart Technologies, Moscow Polytechnic University, St. Bolshaya Semenovskaya, 38, 107023 Moscow, Russia
- Faculty of Transport, North-Eastern Federal University, St. Belinsky, 58, 677000 Yakutsk, Russia
| | - Insaf Ullah
- Department of Electrical Engineering, Hamdard Institute of Engineering and Technology, Hamdard University, Islamabad 44000, Pakistan
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2
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Kumar K, Chaudhri SN, Rajput NS, Shvetsov AV, Sahal R, Alsamhi SH. An IoT-Enabled E-Nose for Remote Detection and Monitoring of Airborne Pollution Hazards Using LoRa Network Protocol. Sensors (Basel) 2023; 23:4885. [PMID: 37430799 DOI: 10.3390/s23104885] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/12/2023]
Abstract
Detection and monitoring of airborne hazards using e-noses has been lifesaving and prevented accidents in real-world scenarios. E-noses generate unique signature patterns for various volatile organic compounds (VOCs) and, by leveraging artificial intelligence, detect the presence of various VOCs, gases, and smokes onsite. Widespread monitoring of airborne hazards across many remote locations is possible by creating a network of gas sensors using Internet connectivity, which consumes significant power. Long-range (LoRa)-based wireless networks do not require Internet connectivity while operating independently. Therefore, we propose a networked intelligent gas sensor system (N-IGSS) which uses a LoRa low-power wide-area networking protocol for real-time airborne pollution hazard detection and monitoring. We developed a gas sensor node by using an array of seven cross-selective tin-oxide-based metal-oxide semiconductor (MOX) gas sensor elements interfaced with a low-power microcontroller and a LoRa module. Experimentally, we exposed the sensor node to six classes i.e., five VOCs plus ambient air and as released by burning samples of tobacco, paints, carpets, alcohol, and incense sticks. Using the proposed two-stage analysis space transformation approach, the captured dataset was first preprocessed using the standardized linear discriminant analysis (SLDA) method. Four different classifiers, namely AdaBoost, XGBoost, Random Forest (RF), and Multi-Layer Perceptron (MLP), were then trained and tested in the SLDA transformation space. The proposed N-IGSS achieved "all correct" identification of 30 unknown test samples with a low mean squared error (MSE) of 1.42 × 10-4 over a distance of 590 m.
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Affiliation(s)
- Kanak Kumar
- Department of Electronics Engineering, Indian Institute of Technology (BHU), Varanasi 221005, India
| | - Shiv Nath Chaudhri
- Department of Electronics Engineering, Indian Institute of Technology (BHU), Varanasi 221005, India
- Department of Electronics and Communication Engineering, Santhiram Engineering College, Nandyal 518501, India
| | - Navin Singh Rajput
- Department of Electronics Engineering, Indian Institute of Technology (BHU), Varanasi 221005, India
| | - Alexey V Shvetsov
- Department of Smart Technologies, Moscow Polytechnic University, 107023 Moscow, Russia
- Department of Transport, North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Radhya Sahal
- School of Computer Science and IT, University College Cork, T12 K8AF Cork, Ireland
- Faculty of Computer Science and Engineering, Hodeidah University, Al Hodeidah P.O. Box 3114, Yemen
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3
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Mohsan SAH, Sadiq M, Li Y, Shvetsov AV, Shvetsova SV, Shafiq M. NOMA-Based VLC Systems: A Comprehensive Review. Sensors (Basel) 2023; 23:2960. [PMID: 36991671 PMCID: PMC10051813 DOI: 10.3390/s23062960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/05/2023] [Accepted: 02/13/2023] [Indexed: 06/19/2023]
Abstract
The enhanced proliferation of connected entities needs a deployment of innovative technologies for the next generation wireless networks. One of the critical concerns, however, is the spectrum scarcity, due to the unprecedented broadcast penetration rate nowadays. Based on this, visible light communication (VLC) has recently emerged as a viable solution to secure high-speed communications. VLC, a high data rate communication technology, has proven its stature as a promising complementary to its radio frequency (RF) counterpart. VLC is a cost-effective, energy-efficient, and secure technology that exploits the current infrastructure, specifically within indoor and underwater environments. Yet, despite their appealing capabilities, VLC systems face several limitations which constraint their potentials such as LED's limited bandwidth, dimming, flickering, line-of-sight (LOS) requirement, impact of harsh weather conditions, noise, interference, shadowing, transceiver alignment, signal decoding complexity, and mobility issue. Consequently, non-orthogonal multiple access (NOMA) has been considered an effective technique to circumvent these shortcomings. The NOMA scheme has emerged as a revolutionary paradigm to address the shortcomings of VLC systems. The potentials of NOMA are to increase the number of users, system's capacity, massive connectivity, and enhance the spectrum and energy efficiency in future communication scenarios. Motivated by this, the presented study offers an overview of NOMA-based VLC systems. This article provides a broad scope of existing research activities of NOMA-based VLC systems. This article aims to provide firsthand knowledge of the prominence of NOMA and VLC and surveys several NOMA-enabled VLC systems. We briefly highlight the potential and capabilities of NOMA-based VLC systems. In addition, we outline the integration of such systems with several emerging technologies such as intelligent reflecting surfaces (IRS), orthogonal frequency division multiplexing (OFDM), multiple-input and multiple-output (MIMO) and unmanned aerial vehicles (UAVs). Furthermore, we focus on NOMA-based hybrid RF/VLC networks and discuss the role of machine learning (ML) tools and physical layer security (PLS) in this domain. In addition, this study also highlights diverse and significant technical hindrances prevailing in NOMA-based VLC systems. We highlight future research directions, along with provided insights that are envisioned to be helpful towards the effective practical deployment of such systems. In a nutshell, this review highlights the existing and ongoing research activities for NOMA-based VLC systems, which will provide sufficient guidelines for research communities working in this domain and it will pave the way for successful deployment of these systems.
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Affiliation(s)
- Syed Agha Hassnain Mohsan
- Optical Communications Laboratory, Ocean College, Zhejiang University, Zheda Road 1, Zhoushan 316021, China
| | - Muhammad Sadiq
- Shenzhen Institute of Information Technology, Shenzhen 518172, China
| | - Yanlong Li
- Optical Communications Laboratory, Ocean College, Zhejiang University, Zheda Road 1, Zhoushan 316021, China
- Ministry of Education Key Laboratory of Cognitive Radio and Information Processing, Guilin University of Electronic Technology, Guilin 541004, China
| | - Alexey V. Shvetsov
- Department of Smart Technologies, Moscow Polytechnic University, 107023 Moscow, Russia
- Faculty of Road Transport, North-Eastern Federal University, 107023 Yakutsk, Russia
| | | | - Muhammad Shafiq
- Cyberspace Institute of Advanced Technology, Guangzhou University, Guangzhou 510006, China
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Mohsan SAH, Li Y, Shvetsov AV, Varela-Aldás J, Mostafa SM, Elfikky A. A Survey of Deep Learning Based NOMA: State of the Art, Key Aspects, Open Challenges and Future Trends. Sensors (Basel) 2023; 23:2946. [PMID: 36991657 PMCID: PMC10058127 DOI: 10.3390/s23062946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Non-Orthogonal Multiple Access (NOMA) has become a promising evolution with the emergence of fifth-generation (5G) and Beyond-5G (B5G) rollouts. The potentials of NOMA are to increase the number of users, the system's capacity, massive connectivity, and enhance the spectrum and energy efficiency in future communication scenarios. However, the practical deployment of NOMA is hindered by the inflexibility caused by the offline design paradigm and non-unified signal processing approaches of different NOMA schemes. The recent innovations and breakthroughs in deep learning (DL) methods have paved the way to adequately address these challenges. The DL-based NOMA can break these fundamental limits of conventional NOMA in several aspects, including throughput, bit-error-rate (BER), low latency, task scheduling, resource allocation, user pairing and other better performance characteristics. This article aims to provide firsthand knowledge of the prominence of NOMA and DL and surveys several DL-enabled NOMA systems. This study emphasizes Successive Interference Cancellation (SIC), Channel State Information (CSI), impulse noise (IN), channel estimation, power allocation, resource allocation, user fairness and transceiver design, and a few other parameters as key performance indicators of NOMA systems. In addition, we outline the integration of DL-based NOMA with several emerging technologies such as intelligent reflecting surfaces (IRS), mobile edge computing (MEC), simultaneous wireless and information power transfer (SWIPT), Orthogonal Frequency Division Multiplexing (OFDM), and multiple-input and multiple-output (MIMO). This study also highlights diverse, significant technical hindrances in DL-based NOMA systems. Finally, we identify some future research directions to shed light on paramount developments needed in existing systems as a probable to invigorate further contributions for DL-based NOMA system.
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Affiliation(s)
- Syed Agha Hassnain Mohsan
- Optical Communications Laboratory, Ocean College, Zhejiang University, Zheda Road 1, Zhoushan 316021, China
| | - Yanlong Li
- Optical Communications Laboratory, Ocean College, Zhejiang University, Zheda Road 1, Zhoushan 316021, China
- Ministry of Education Key Laboratory of Cognitive Radio and Information Processing, Guilin University of Electronic Technology, Guilin 541004, China
| | - Alexey V. Shvetsov
- Department of Smart Technologies, Moscow Polytechnic University, Moscow 107023, Russia
- Faculty of Transport Technologies, North-Eastern Federal University, Yakutsk 677000, Russia
| | - José Varela-Aldás
- Centro de Investigaciones de Ciencias Humanas y de la Educación (CICHE), Universidad Indoamérica, Ambato 180103, Ecuador
| | - Samih M. Mostafa
- Computer Science Department, Faculty of Computers and Information, South Valley University, Qena 83523, Egypt
| | - Abdelrahman Elfikky
- College of Engineering, Arab Academy for Science, Technology and Maritime Transport, Alexandria 21500, Egypt
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5
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Egorov VV, Shvetsov AV, Pichkur EB, Shaldzhyan AA, Zabrodskaya YA, Vinogradova DS, Nekrasov PA, Gorshkov AN, Garmay YP, Kovaleva AA, Stepanova LA, Tsybalova LM, Shtam TA, Myasnikov AG, Konevega AL. Inside and outside of virus-like particles HBc and HBc/4M2e: A comprehensive study of the structure. Biophys Chem 2023; 293:106943. [PMID: 36495688 DOI: 10.1016/j.bpc.2022.106943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/11/2022]
Abstract
Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) form virus-like particles whose structure was studied using a combination of molecular modeling and cryo-electron microscopy (cryo-EM). It was also shown that self-assembling of the particles occurs inside bacterial cells, but despite the big inner volume of the core shell particle, purified HBc/4M2e contain an insignificant amount of bacterial proteins. It was shown that a fragment of the M2e corresponding to 4M2e insertion is prone to formation of amyloid-like fibrils. However, as the part of the immunodominant loop, M2e insertion does not show a tendency to intermolecular interaction. A full-atomic HBc-4M2e model with the resolution of about 3 Å (3.13 Å for particles of Т = 4 symmetry, 3.7 Å for particles of Т = 3 symmetry) was obtained by molecular modeling methods based on cryo-EM data.
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Affiliation(s)
- V V Egorov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation; Institute of Experimental Medicine, Academika Pavlova, 12, 197376 St. Petersburg, Russian Federation.
| | - A V Shvetsov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation; Peter the Great St.Petersburg Polytechnic University, Politehnicheskaya 29, St. Petersburg, Russian Federation
| | - E B Pichkur
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation
| | - A A Shaldzhyan
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - Ya A Zabrodskaya
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation; Peter the Great St.Petersburg Polytechnic University, Politehnicheskaya 29, St. Petersburg, Russian Federation
| | - D S Vinogradova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation
| | - P A Nekrasov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - A N Gorshkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - Yu P Garmay
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation
| | - A A Kovaleva
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - L A Stepanova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - L M Tsybalova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - T A Shtam
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation
| | - A G Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation
| | - A L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation; Peter the Great St.Petersburg Polytechnic University, Politehnicheskaya 29, St. Petersburg, Russian Federation
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Chaudhri SN, Rajput NS, Alsamhi SH, Shvetsov AV, Almalki FA. Zero-Padding and Spatial Augmentation-Based Gas Sensor Node Optimization Approach in Resource-Constrained 6G-IoT Paradigm. Sensors (Basel) 2022; 22:s22083039. [PMID: 35459024 PMCID: PMC9028001 DOI: 10.3390/s22083039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/17/2022] [Accepted: 04/13/2022] [Indexed: 12/16/2022]
Abstract
Ultra-low-power is a key performance indicator in 6G-IoT ecosystems. Sensor nodes in this eco-system are also capable of running light-weight artificial intelligence (AI) models. In this work, we have achieved high performance in a gas sensor system using Convolutional Neural Network (CNN) with a smaller number of gas sensor elements. We have identified redundant gas sensor elements in a gas sensor array and removed them to reduce the power consumption without significant deviation in the node’s performance. The inevitable variation in the performance due to removing redundant sensor elements has been compensated using specialized data pre-processing (zero-padded virtual sensors and spatial augmentation) and CNN. The experiment is demonstrated to classify and quantify the four hazardous gases, viz., acetone, carbon tetrachloride, ethyl methyl ketone, and xylene. The performance of the unoptimized gas sensor array has been taken as a “baseline” to compare the performance of the optimized gas sensor array. Our proposed approach reduces the power consumption from 10 Watts to 5 Watts; classification performance sustained to 100 percent while quantification performance compensated up to a mean squared error (MSE) of 1.12 × 10−2. Thus, our power-efficient optimization paves the way to “computation on edge”, even in the resource-constrained 6G-IoT paradigm.
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Affiliation(s)
- Shiv Nath Chaudhri
- Department of Electronics Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India;
| | - Navin Singh Rajput
- Department of Electronics Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India;
- Correspondence:
| | - Saeed Hamood Alsamhi
- Software Research Institute, Technological University of the Shannon, Midlands Midwest, N37HD68 Athlone, Ireland;
- Faculty of Engineering, IBB University, Ibb 70270, Yemen
| | - Alexey V. Shvetsov
- Department of Operation of Road Transport and Car Service, North-Eastern Federal University, 677000 Yakutsk, Russia;
- Department of Transport and Technological Processes, Vladivostok State University of Economics and Service, 690014 Vladivostok, Russia
| | - Faris A. Almalki
- Department of Computer Engineering, College of Computers and Information Technology, Taif University, Taif 21944, Saudi Arabia;
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Zabrodskaya YA, Egorov VV, Sokolov AV, Shvetsov AV, Gorshkova YE, Ivankov OI, Kostevich VA, Gorbunov NP, Ramsay ES, Fedorova ND, Bondarenko AB, Vasilyev VB. Caught red handed: modeling and confirmation of the myeloperoxidase ceruloplasmin alpha-thrombin complex. Biometals 2022; 35:1157-1168. [PMID: 35962914 PMCID: PMC9375587 DOI: 10.1007/s10534-022-00432-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
The work is devoted to the study of the structural characteristics of the myeloperoxidase-ceruloplasmin-thrombin complex using small-angle neutron scattering methods in combination with computer modeling, as well as surface plasmon resonance and solid-phase enzyme assay. We have previously shown that the functioning of active myeloperoxidase during inflammation, despite the presence in the blood of an excess of ceruloplasmin which inhibits its activity, is possible due to the partial proteolysis of ceruloplasmin by thrombin. In this study, the myeloperoxidase-ceruloplasmin-thrombin heterohexamer was obtained in vitro. The building of a heterohexamer full-atomic model in silico, considering the glycosylation of the constituent proteins, confirmed the absence of steric barriers for the formation of protein-protein contacts. It was shown that the partial proteolysis of ceruloplasmin does not affect its ability to bind to myeloperoxidase, and a structural model of the heterohexamer was obtained using the small-angle neutron scattering method.
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Affiliation(s)
- Yana A. Zabrodskaya
- grid.415738.c0000 0000 9216 2496Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg, Russia 197376 ,grid.32495.390000 0000 9795 6893Peter the Great Saint Petersburg Polytechnic University, 29 Ulitsa Polytechnicheskaya, St. Petersburg, Russia 194064 ,grid.18919.380000000406204151Petersburg Nuclear Physics Institute Named by B. P. Konstantinov of National Research Center, Kurchatov Institute, 1 mkr. Orlova roshcha, Gatchina, Russia 188300 ,grid.452514.30000 0004 0494 5466Department of Molecular Virology Smorodintsev Research Institute of Influenza (Div. Russian Ministry of Health), 15/17 Ulitsa Professora Popova, St. Petersburg, Russia 197376
| | - Vladimir V. Egorov
- grid.415738.c0000 0000 9216 2496Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg, Russia 197376 ,grid.465311.40000 0004 0482 8489Institute of Experimental Medicine, 12 Ulitsa Akademika Pavlova, St. Petersburg, Russia 197376
| | - Alexey V. Sokolov
- grid.465311.40000 0004 0482 8489Institute of Experimental Medicine, 12 Ulitsa Akademika Pavlova, St. Petersburg, Russia 197376
| | - Alexey V. Shvetsov
- grid.32495.390000 0000 9795 6893Peter the Great Saint Petersburg Polytechnic University, 29 Ulitsa Polytechnicheskaya, St. Petersburg, Russia 194064 ,grid.18919.380000000406204151Petersburg Nuclear Physics Institute Named by B. P. Konstantinov of National Research Center, Kurchatov Institute, 1 mkr. Orlova roshcha, Gatchina, Russia 188300
| | - Yulia E. Gorshkova
- grid.33762.330000000406204119International Intergovernmental Organization Joint Institute for Nuclear Research, 6 Ulitsa Joliot-Curie, Dubna, Russia 141980 ,grid.77268.3c0000 0004 0543 9688Kazan Federal University, 18 Ulitsa Kremlyovskaya, Kazan, Russia 420008
| | - Oleksandr I. Ivankov
- grid.33762.330000000406204119International Intergovernmental Organization Joint Institute for Nuclear Research, 6 Ulitsa Joliot-Curie, Dubna, Russia 141980
| | - Valeria A. Kostevich
- grid.465311.40000 0004 0482 8489Institute of Experimental Medicine, 12 Ulitsa Akademika Pavlova, St. Petersburg, Russia 197376
| | - Nikolay P. Gorbunov
- grid.465311.40000 0004 0482 8489Institute of Experimental Medicine, 12 Ulitsa Akademika Pavlova, St. Petersburg, Russia 197376
| | - Edward S. Ramsay
- grid.419591.1Saint Petersburg Pasteur Institute, 14 Ulitsa Mira, St. Petersburg, Russia 197101
| | - Natalya D. Fedorova
- grid.18919.380000000406204151Petersburg Nuclear Physics Institute Named by B. P. Konstantinov of National Research Center, Kurchatov Institute, 1 mkr. Orlova roshcha, Gatchina, Russia 188300
| | - Andrey B. Bondarenko
- grid.415738.c0000 0000 9216 2496Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg, Russia 197376
| | - Vadim B. Vasilyev
- grid.465311.40000 0004 0482 8489Institute of Experimental Medicine, 12 Ulitsa Akademika Pavlova, St. Petersburg, Russia 197376
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Shvetsov AV, Lebedev DV, Zabrodskaya YA, Shaldzhyan AA, Egorova MA, Vinogradova DS, Konevega AL, Gorshkov AN, Ramsay ES, Radulescu A, Sergeeva MV, Plotnikova MA, Komissarov AB, Taraskin AS, Lebedev KI, Garmay YP, Kuznetsov VV, Isaev-Ivanov VV, Vasin AV, Tsybalova LM, Egorov VV. Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain. J Biomol Struct Dyn 2020; 39:4375-4384. [PMID: 32490728 DOI: 10.1080/07391102.2020.1776636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Two influenza A nucleoprotein variants (wild-type: G102R; and mutant: G102R and E292G) were studied with regard to macro-molecular interactions in oligomeric form (24-mers). The E292G mutation has been previously shown to provide cold adaptation. Molecular dynamics simulations of these complexes and trajectory analysis showed that the most significant difference between the obtained models was distance between nucleoprotein complex strands. The isolated complexes of two ribonucleoprotein variants were characterized by transmission electron microscopy and differential scanning fluorimetry (DSF). Presence of the E292G substitution was shown by DSF to affect nucleoprotein complex melting temperature. In the filament interface peptide model, it was shown that the peptide corresponding in primary structure to the wild-type NP (SGYDFEREGYS) is prone to temperature-dependent self-association, unlike the peptide corresponding to E292G substitution (SGYDFGREGYS). It was also shown that the SGYDFEREGYS peptide is capable of interacting with a monomeric nucleoprotein (wild type); this interaction's equilibrium dissociation constant is five orders of magnitude lower than for the SGYDFGREGYS peptide. Using small-angle neutron scattering (SANS), the supramolecular structures of isolated complexes of these proteins were studied at temperatures of 15, 32, and 37 °C. SANS data show that the structures of the studied complexes at elevated temperature differ from the rod-like particle model and react differently to temperature changes. The data suggest that the mechanism behind cold adaptation with E292G is associated with a weakening of the interaction between strands of the ribonucleoprotein complex and, as a result, the appearance of inter-chain interface flexibility necessary for complex function at low temperature.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A V Shvetsov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - D V Lebedev
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - Y A Zabrodskaya
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A A Shaldzhyan
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - M A Egorova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - D S Vinogradova
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,NanoTemper Technologies Rus, St. Petersburg, Russia
| | - A L Konevega
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - A N Gorshkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - E S Ramsay
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A Radulescu
- Jülich Centre, Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Munich, Germany
| | - M V Sergeeva
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - M A Plotnikova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A B Komissarov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A S Taraskin
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - K I Lebedev
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Yu P Garmay
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - V V Kuznetsov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - V V Isaev-Ivanov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - A V Vasin
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,St. Petersburg State Chemical-Pharmaceutical Academy, St. Petersburg, Russia
| | - L M Tsybalova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - V V Egorov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,Federal State Budgetary Scientific Institution "Institute of Experimental Medicine", St. Petersburg, Russia
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9
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Zabrodskaya YA, Shvetsov AV, Tsvetkov VB, Egorov VV. A double-edged sword: supramolecular complexes of triazavirine display multicenter binding effects which influence aggregate formation. J Biomol Struct Dyn 2018; 37:3041-3047. [PMID: 30073907 DOI: 10.1080/07391102.2018.1507837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yana A Zabrodskaya
- a Molecular Biology of Viruses Department, Smorodintsev Research Institute of Influenza , Ministry of Healthcare of the Russian Federation , St. Petersburg , Russia.,b Molecular and Radiation Biophysics Department , Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center "Kurchatov Institute" , Gatchina , Russia
| | - Alexey V Shvetsov
- b Molecular and Radiation Biophysics Department , Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center "Kurchatov Institute" , Gatchina , Russia.,c Supercomputer Center , Peter the Great Saint-Petersburg State Polytechnic University , St. Petersburg , Russia
| | - Vladimir B Tsvetkov
- a Molecular Biology of Viruses Department, Smorodintsev Research Institute of Influenza , Ministry of Healthcare of the Russian Federation , St. Petersburg , Russia.,d Biophysics Department , Research and Clinical Center for Physical Chemical Medicine , Moscow , Russia.,e Polyelectrolytes and Biomedical Polymers Laboratory , A.V. Topchiev Institute of Petrochemical Synthesis , RAS Moscow , Russia
| | - Vladimir V Egorov
- a Molecular Biology of Viruses Department, Smorodintsev Research Institute of Influenza , Ministry of Healthcare of the Russian Federation , St. Petersburg , Russia.,b Molecular and Radiation Biophysics Department , Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center "Kurchatov Institute" , Gatchina , Russia.,f Molecular Genetics Department , Federal State Budgetary Scientific Institution "Institute of Experimental Medicine" , St. Petersburg , Russia
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10
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Shvetsov AV, Zabrodskaya YA, Nekrasov PA, Egorov VV. Triazavirine supramolecular complexes as modifiers of the peptide oligomeric structure. J Biomol Struct Dyn 2017; 36:2694-2698. [PMID: 28828928 DOI: 10.1080/07391102.2017.1367329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In this study, we present molecular dynamics simulations of the antiviral drug triazavirine, that affects formation of amyloid-like fibrils of the model peptide (SI). According to our simulations, triazavirine is able to form linear supramolecular structures which can act as shields and prevent interactions between SI monomers. This model, as validated by simulations, provides an adequate explanation of triazavirine's mechanism of action as it pertains to SI peptide fibril formation.
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Affiliation(s)
- Alexey V Shvetsov
- a Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute" , Orlova Roscha, 188300 Gatchina , Russia .,b Peter the Great Saint-Petersburg Polytechnic University , 29, Politekhnicheskaya, 194064 St. Petersburg , Russia
| | - Yana A Zabrodskaya
- c Research Institute of Influenza, Ministry of Healthcare of the Russian Federation , 15/17, Prof. Popova, 197376 St. Petersburg , Russia
| | - Peter A Nekrasov
- c Research Institute of Influenza, Ministry of Healthcare of the Russian Federation , 15/17, Prof. Popova, 197376 St. Petersburg , Russia
| | - Vladimir V Egorov
- a Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute" , Orlova Roscha, 188300 Gatchina , Russia .,c Research Institute of Influenza, Ministry of Healthcare of the Russian Federation , 15/17, Prof. Popova, 197376 St. Petersburg , Russia .,d Federal State Budgetary Scientific "Institute of Experimental Medicine" , 12, Akad. Pavlova, 197376 St. Petersburg , Russia
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11
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Rychkov GN, Ilatovskiy AV, Nazarov IB, Shvetsov AV, Lebedev DV, Konev AY, Isaev-Ivanov VV, Onufriev AV. Partially Assembled Nucleosome Structures at Atomic Detail. Biophys J 2016; 112:460-472. [PMID: 28038734 DOI: 10.1016/j.bpj.2016.10.041] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/06/2016] [Accepted: 10/28/2016] [Indexed: 11/29/2022] Open
Abstract
The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.
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Affiliation(s)
- Georgy N Rychkov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Institute of Physics, Nanotechnology and Telecommunications, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Andrey V Ilatovskiy
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Igor B Nazarov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexey V Shvetsov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Institute of Applied Mathematics and Mechanics, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Dmitry V Lebedev
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Alexander Y Konev
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Vladimir V Isaev-Ivanov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Alexey V Onufriev
- Departments of Computer Science and Physics, Virginia Tech, Blacksburg, Virginia.
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12
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Kudrin AV, Plankina SM, Vikhrova OV, Nezhdanov AV, Mashin AI, Drozdov YN, Shvetsov AV. Characterization of the cleaved edge cross section of the heterostructures with GaMnAs layer by the confocal micro-Raman spectroscopy. Micron 2016; 93:38-42. [PMID: 27912140 DOI: 10.1016/j.micron.2016.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 11/19/2022]
Abstract
Confocal micro-Raman spectroscopy was used to measure cross-section linescans of the cleaved edge of heterostructures involving a GaMnAs layer. The investigations revealed a shift of the TO mode in the compressed GaMnAs layer to high frequencies relative to the TO GaAs mode in the substrate and to low frequencies in the tensile GaMnAs layers. These results are in agreement with the different manifestations of the anomalous Hall effect in the GaMnAs layers, with either compressive or tensile strains. It is shown that Raman spectroscopy is an appropriate method for the investigation of cross-sectional semiconductor heterostructures whose total thickness is comparable to the size of the analyzing laser spot.
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Affiliation(s)
- A V Kudrin
- Lobachevsky State University of Nizhny Novgorod, Gagarina pr. 23/3, 603950 Nizhny Novgorod, Russia.
| | - S M Plankina
- Lobachevsky State University of Nizhny Novgorod, Gagarina pr. 23/3, 603950 Nizhny Novgorod, Russia
| | - O V Vikhrova
- Lobachevsky State University of Nizhny Novgorod, Gagarina pr. 23/3, 603950 Nizhny Novgorod, Russia
| | - A V Nezhdanov
- Lobachevsky State University of Nizhny Novgorod, Gagarina pr. 23/3, 603950 Nizhny Novgorod, Russia
| | - A I Mashin
- Lobachevsky State University of Nizhny Novgorod, Gagarina pr. 23/3, 603950 Nizhny Novgorod, Russia
| | - Yu N Drozdov
- Institute for Physics of Microstructures, RAS, 603950 Nizhny Novgorod, Russia
| | - A V Shvetsov
- Lobachevsky State University of Nizhny Novgorod, Gagarina pr. 23/3, 603950 Nizhny Novgorod, Russia
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13
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Shvetsov AV, Dyuzhikova NA, Savenko YN, Batotsyrenova EG, Kashuro VA. Effects of Experimental Coma on the Expression of Bcl-2 Protein and Caspases 3 and 9 in Rat Brain. Bull Exp Biol Med 2015; 160:216-8. [PMID: 26645287 DOI: 10.1007/s10517-015-3132-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 11/24/2022]
Abstract
We performed immunohistochemical analysis of the expression of caspases 3, 9 and bcl-2 protein in rat brain at various terms after administration of LD50 of sodium thiopental. Expression of the specified apoptosis markers was found in the sensorimotor cortex and hippocampus (dentate gyrus and CA2 region).
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Affiliation(s)
- A V Shvetsov
- Laboratory of Genetics of Higher Nervous Activity, I. P. Pavlov Institute of Physiology, Russian Academy of Sciences, St. Petersburg, Russia. .,Laboratory of Biochemical Toxicology and Pharmacology, Institute of Toxicology, Federal Medical-Biological Agency of Russia, St. Petersburg, Russia.
| | - N A Dyuzhikova
- Laboratory of Biochemical Toxicology and Pharmacology, Institute of Toxicology, Federal Medical-Biological Agency of Russia, St. Petersburg, Russia
| | - Yu N Savenko
- Laboratory of Biochemical Toxicology and Pharmacology, Institute of Toxicology, Federal Medical-Biological Agency of Russia, St. Petersburg, Russia
| | - E G Batotsyrenova
- Laboratory of Genetics of Higher Nervous Activity, I. P. Pavlov Institute of Physiology, Russian Academy of Sciences, St. Petersburg, Russia
| | - V A Kashuro
- Laboratory of Genetics of Higher Nervous Activity, I. P. Pavlov Institute of Physiology, Russian Academy of Sciences, St. Petersburg, Russia
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14
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Shvetsov AV, Lebedev DV, Chervyakova DB, Bakhlanova IV, Yung IA, Radulescu A, Kuklin AI, Baitin DM, Isaev-Ivanov VV. Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering. FEBS Lett 2014; 588:948-55. [PMID: 24530684 DOI: 10.1016/j.febslet.2014.01.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 01/17/2014] [Accepted: 01/28/2014] [Indexed: 11/18/2022]
Abstract
Using molecular modeling techniques we have built the full atomic structure and performed molecular dynamics simulations for the complexes formed by Escherichia coli RecX protein with a single-stranded oligonucleotide and with RecA presynaptic filament. Based on the modeling and SANS experimental data a sandwich-like filament structure formed two chains of RecX monomers bound to the opposite sides of the single stranded DNA is proposed for RecX::ssDNA complex. The model for RecX::RecA::ssDNA include RecX binding into the grove of RecA::ssDNA filament that occurs mainly via Coulomb interactions between RecX and ssDNA. Formation of RecX::RecA::ssDNA filaments in solution was confirmed by SANS measurements which were in agreement with the spectra computed from the molecular dynamics simulations.
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Affiliation(s)
- Alexey V Shvetsov
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; St. Petersburg State Polytechnical University, St. Petersburg, Russia.
| | - Dmitry V Lebedev
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia.
| | - Daria B Chervyakova
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Irina V Bakhlanova
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Igor A Yung
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; St. Petersburg State Polytechnical University, St. Petersburg, Russia
| | - Aurel Radulescu
- Jülich Centre for Neutron Science Outstation at FRM II, Garching, Germany
| | | | - Dmitry M Baitin
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; St. Petersburg State Polytechnical University, St. Petersburg, Russia
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15
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Shvetsov AV, Zachepilo TG, Vaĭdo AI, Kamyshev NG, Lopatina NG. [On epigenetic regulation of process of formation of long-term memory]. Zh Evol Biokhim Fiziol 2013; 49:97-104. [PMID: 23789394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The review summarizes current concepts on role of several covalent posttranslation chromatin modifications in the process of memory formation in vertebrate and invertebrate animals. There is described a chain of intracellular events from activation of receptors and signal pathways to change of the functional state of genome.
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16
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Shvetsov AV, Zachepilo TG. [The morphological basis of conditioned reflex in the honeybee Apis mellifera L]. Zh Vyssh Nerv Deiat Im I P Pavlova 2012; 62:654-663. [PMID: 23530444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A review. Works related to research into the neuroanatomical basis of associative learning in the honeybee (proboscis extension reflex) are summarized. Data on the brain organization of the honeybee are presented. The parallel neural pathways of conditioned and unconditioned stimuli are shown. Contribution of different brain structures and identified neurons (VUMmx1, PE1) in the formation of the proboscis extension reflex are discussed.
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17
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Dudkina AV, Shvetsov AV, Bakhlanova IV, Baĭtin DM. [Changing of filamentation dynamics of RecA protein, induced by D112R amino acid substitution or ATP to dATP replacement, results in filament steadiness TO THE RecX protein action]. Mol Biol (Mosk) 2011; 45:546-553. [PMID: 21790018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
It is known that RecX is a negative regulator of RecA protein. We found that the mutant RecA D112R protein exhibits increased resistance to RecX protein comparatively to wild-type RecA protein in vitro and in vivo. Using molecular modeling we showed, that amino acid located in position 112 can not approach RecX closer than 25-28 angstroms. Thus, direct contact between amino acid and RecX is impossible. RecA D112R protein more actively competes with SSB protein for the binding sites on ssDNA and, therefore, differs from the wild-type RecA protein by dynamics of filamentation on ssDNA. On the other hand, after the replacement of ATP by dATP, the wild-type RecA protein, changing the dynamics of filamentation on ssDNA, also becomes more resistant to RecX. Based on these data it is concluded that the dynamics of filamentation has a great, if not dominant role in the stability of RecA filament to RecX relative to the role of RecA-RecX protein-protein interactions discussed earlier. We also propose an improved model of regulation of RecA by RecX protein, where RecA filament elongation along ssDNA is blocked by RecX protein on the ssDNA region, located outside the filament.
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18
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Surzhik MA, Churkina SV, Shmidt AE, Shvetsov AV, Kozhina TN, Firsov DL, Firsov LM, Petukhov MG. [The effect of point amino acid substitutions in an internal alpha-helix on thermostability of Aspergillus awamori X100 glucoamylase]. Prikl Biokhim Mikrobiol 2010; 46:221-227. [PMID: 20391767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Conformational flexibility of alpha-helices in glucoamylase of the fungus Aspergillus awamori was studied by molecular dynamics methods. Several amino acid substitutions (G127A, P128A, I136L, G137A, and G139A) optimizing intrinsic interactions in one of the alpha-helices (D) within the hydrophobic core of this protein were constructed and studied. It was found that these point mutations had different effects on the glucoamylase thermal inactivation constant. Unlike amino acid substitution P128A and substitutions G137A and A246C, I136L and G139A displayed a pronounced additive thermostabilizing effect.
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19
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Shvetsov AV. [The flees fauna on small mammals in the steppe landscapes of the Orenburg Region]. Med Parazitol (Mosk) 2009:45-46. [PMID: 20120378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Shvetsov AV, Bystrov IV. [Fleas of small mammals in the steppe zone of the Southern Urals]. Med Parazitol (Mosk) 2007:35-9. [PMID: 17912833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
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