1
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Cao C, Zhang G, Li X, Wang Y, Lü J. Nanomechanical collective vibration of SARS-CoV-2 spike proteins. J Mol Recognit 2024; 37:e3091. [PMID: 38773782 DOI: 10.1002/jmr.3091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/08/2024] [Accepted: 05/12/2024] [Indexed: 05/24/2024]
Abstract
The development of effective therapeutics against COVID-19 requires a thorough understanding of the receptor recognition mechanism of the SARS-CoV-2 spike (S) protein. Here the multidomain collective dynamics on the trimer of the spike protein has been analyzed using normal mode analysis (NMA). A common nanomechanical profile was identified in the spike proteins of SARS-CoV-2 and its variants. The profile involves collective vibrations of the receptor-binding domain (RBD) and the N-terminal domain (NTD), which may mediate the physical interaction process. Quantitative analysis of the collective modes suggests a nanomechanical property involving large-scale conformational changes, which explains the difference in receptor binding affinity among different variants. These results support the use of intrinsic global dynamics as a valuable perspective for studying the allosteric and functional mechanisms of the S protein. This approach also provides a low-cost theoretical toolkit for screening potential pathogenic mutations and drug targets.
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Affiliation(s)
- Changfeng Cao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guangxu Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- College of Pharmacy, Binzhou Medical University, Yantai, China
| | - Xueling Li
- College of Public Health, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Yadi Wang
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- College of Pharmacy, Binzhou Medical University, Yantai, China
| | - Junhong Lü
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- College of Pharmacy, Binzhou Medical University, Yantai, China
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2
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Nonn A, Kiss B, Pezeshkian W, Tancogne-Dejean T, Cerrone A, Kellermayer M, Bai Y, Li W, Wierzbicki T. Inferring mechanical properties of the SARS-CoV-2 virus particle with nano-indentation tests and numerical simulations. J Mech Behav Biomed Mater 2023; 148:106153. [PMID: 37865016 DOI: 10.1016/j.jmbbm.2023.106153] [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: 08/11/2023] [Revised: 09/14/2023] [Accepted: 09/27/2023] [Indexed: 10/23/2023]
Abstract
The pandemic caused by the SARS-CoV-2 virus has claimed more than 6.5 million lives worldwide. This global challenge has led to accelerated development of highly effective vaccines tied to their ability to elicit a sustained immune response. While numerous studies have focused primarily on the spike (S) protein, less is known about the interior of the virus. Here we propose a methodology that combines several experimental and simulation techniques to elucidate the internal structure and mechanical properties of the SARS-CoV-2 virus. The mechanical response of the virus was analyzed by nanoindentation tests using a novel flat indenter and evaluated in comparison to a conventional sharp tip indentation. The elastic properties of the viral membrane were estimated by analytical solutions, molecular dynamics (MD) simulations on a membrane patch and by a 3D Finite Element (FE)-beam model of the virion's spike protein and membrane molecular structure. The FE-based inverse engineering approach provided a reasonable reproduction of the mechanical response of the virus from the sharp tip indentation and was successfully verified against the flat tip indentation results. The elastic modulus of the viral membrane was estimated in the range of 7-20 MPa. MD simulations showed that the presence of proteins significantly reduces the fracture strength of the membrane patch. However, FE simulations revealed an overall high fracture strength of the virus, with a mechanical behavior similar to the highly ductile behavior of engineering metallic materials. The failure mechanics of the membrane during sharp tip indentation includes progressive damage combined with localized collapse of the membrane due to severe bending. Furthermore, the results support the hypothesis of a close association of the long membrane proteins (M) with membrane-bound hexagonally packed ribonucleoproteins (RNPs). Beyond improved understanding of coronavirus structure, the present findings offer a knowledge base for the development of novel prevention and treatment methods that are independent of the immune system.
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Affiliation(s)
- Aida Nonn
- CMM Lab, Faculty of Mechanical Engineering, OTH Regensburg, 93053, Regensburg, Germany.
| | - Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, H-1094, Hungary; ELKH-SE Biophysical Virology Research Group, Budapest, H-1094, Hungary
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark
| | | | - Albert Cerrone
- Computational Hydraulics Laboratory, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Miklos Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, H-1094, Hungary; ELKH-SE Biophysical Virology Research Group, Budapest, H-1094, Hungary
| | - Yuanli Bai
- Department of Mechanical and Aerospace of Engineering, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL, 32816, USA
| | - Wei Li
- Impact and Crashworthiness Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tomasz Wierzbicki
- Impact and Crashworthiness Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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3
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Maroli N. Riding the Wave: Unveiling the Conformational Waves from RBD of SARS-CoV-2 Spike Protein to ACE2. J Phys Chem B 2023; 127:8525-8536. [PMID: 37769161 DOI: 10.1021/acs.jpcb.3c04366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
The binding affinity between angiotensin-converting enzyme 2 (ACE2) and the receptor-binding domain (RBD) plays a crucial role in the transmission and reinfection of SARS-CoV2. Here, microsecond molecular dynamics simulations revealed that point mutations in the RBD domain induced conformational transitions that determined the binding affinity between ACE2 and RBD. These structural changes propagated through the RBD domain, altering the orientation of both ACE2 and RBD residues at the binding site. ACE2 receptor shows significant structural heterogeneity, whereas its binding to the RBD domain indicates a much greater degree of structural homogeneity. The receptor was more flexible in its unbound state with the binding of RBD domains inducing structural transitions. The structural heterogeneity observed in the ACE2 unbound form plays a role in the promiscuity of viral entry, as it may allow the receptor to interact with various related and unrelated ligands. Furthermore, rigidity may be important for stabilizing the complex and ensuring the proper orientation of the RBD-binding interface with ACE2. The greater structural homogeneity observed in the ACE2-RBD complex revealed the effectiveness of neutralizing antibodies and vaccines that are primarily directed toward the RBD-binding interface. The binding of the B38 monoclonal antibody revealed restricted conformational transitions in the RBD and ACE2 receptors, attributed to its potent binding interaction.
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Affiliation(s)
- Nikhil Maroli
- Centre for Computational Modeling, Chennai Institute of Technology, Chennai, Tamil Nadu 600069, India
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4
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Tang M, Suraweera A, Nie X, Li Z, Lai P, Wells JW, O'Byrne KJ, Woods RJ, Bolderson E, Richard DJ. Mono-phosphorylation at Ser4 of barrier-to-autointegration factor (Banf1) significantly reduces its DNA binding capability by inducing critical changes in its local conformation and DNA binding surface. Phys Chem Chem Phys 2023; 25:24657-24677. [PMID: 37665626 DOI: 10.1039/d3cp02302h] [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: 09/05/2023]
Abstract
Barrier-to-autointegration factor (Banf1) is a small DNA-bridging protein. The binding status of Banf1 to DNA is regulated by its N-terminal phosphorylation and dephosphorylation, which plays a critical role in cell proliferation. Banf1 can be phosphorylated at Ser4 into mono-phosphorylated Banf1, which is further phosphorylated at Thr3 to form di-phosphorylated Banf1. It was observed decades ago that mono-phosphorylated Banf1 cannot bind to DNA. However, the underlying molecular- and atomic-level mechanisms remain unclear. A clear understanding of these mechanisms will aid in interfering with the cell proliferation process for better global health. Herein, we explored the detailed atomic bases of unphosphorylated Banf1-DNA binding and how mono- and di-phosphorylation of Banf1 impair these atomic bases to eliminate its DNA-binding capability, followed by exploring the DNA-binding capability of mono- and di-phosphorylation Banf1, using comprehensive and systematic molecular modelling and molecular dynamics simulations. This work presented in detail the residue-level binding energies, hydrogen bonds and water bridges between Banf1 and DNA, some of which have not been reported. Moreover, we revealed that mono-phosphorylation of Banf1 causes its N-terminal secondary structure changes, which in turn induce significant changes in Banf1's DNA binding surface, thus eliminating its DNA-binding capability. At the atomic level, we also uncovered the alterations in interactions due to the induction of mono-phosphorylation that result in the N-terminal secondary structure changes of Banf1. Additionally, our modelling showed that phosphorylated Banf1 with their dominant N-terminal secondary structures bind to DNA with a significantly lower affinity and the docked binding pose are not stable in MD simulations. These findings help future studies in predicting effect of mutations in Banf1 on its DNA-binding capability and open a novel avenue for the development of therapeutics such as cancer drugs, targeting cell proliferation by inducing conformational changes in Banf1's N-terminal domain.
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Affiliation(s)
- Ming Tang
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- Faculty of Medicine, Frazer Institute, The University of Queensland at the Translational Research Institute Australia, Brisbane, Australia
| | - Amila Suraweera
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
| | - Xuqiang Nie
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- College of Pharmacy, Key Lab of the Basic Pharmacology of the Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Zilin Li
- School of Mechanics and Safety Engineering, Zhengzhou University, Zhengzhou 450001, China
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, Australia
| | - Pinglin Lai
- Academy of Orthopedics Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - James W Wells
- Faculty of Medicine, Frazer Institute, The University of Queensland at the Translational Research Institute Australia, Brisbane, Australia
| | - Kenneth J O'Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- Princess Alexandra Hospital, Brisbane, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Centre, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Emma Bolderson
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
| | - Derek J Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
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5
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Hu Y, Buehler MJ. End-to-End Protein Normal Mode Frequency Predictions Using Language and Graph Models and Application to Sonification. ACS NANO 2022; 16:20656-20670. [PMID: 36416536 DOI: 10.1021/acsnano.2c07681] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The prediction of mechanical and dynamical properties of proteins is an important frontier, especially given the greater availability of proteins structures. Here we report a series of models that provide end-to-end predictions of nanodynamical properties of proteins, focused on high-throughput normal mode predictions directly from the amino acid sequence. Using neural network models within the family of Natural Language Processing and graph-based methods, we offer atomistically based mechanistic predictions of key protein mechanical features. The models include an end-to-end long short-term memory (LSTM) model, an end-to-end transformer model, a graph-based transformer model, and an equivariant graph neural network. All four models show exceptional performance, with the graph-based transformer architecture offering the best results but at the cost of requiring a graph structure as input. Conversely, the LSTM and transformer models offer end-to-end sequence-to-property prediction capabilities, providing efficient avenues for protein engineering, analysis, and design. We compare our results against published data based on a Principal Neighborhood Aggregation graph neural network, revealing that the transformer model offers better performance while also being able to predict a large set of the first 64 normal mode frequencies, simultaneously. The use of the end-to-end transformer model may facilitate other downstream applications through the use of transfer learning, and it offers a comprehensive prediction of dynamical properties without any structural knowledge, directly from the amino acid sequence. We demonstrate a potential application in scientific sonification, where the normal mode frequencies are transposed to generate audible signals for a detailed analysis of subtle changes of protein sequences.
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Affiliation(s)
- Yiwen Hu
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
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6
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Hu Y, Buehler MJ. Nanomechanical analysis of SARS-CoV-2 variants and predictions of infectiousness and lethality. SOFT MATTER 2022; 18:5833-5842. [PMID: 35899933 PMCID: PMC9364333 DOI: 10.1039/d1sm01181b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
As variants of the pathogen that causes COVID-19 spread around the world, estimates of infectiousness and lethality of newly emerging strains are important. Here we report a predictive model that associates molecular motions and vibrational patterns of the virus spike protein with infectiousness and lethality. The key finding is that most SARS-CoV-2 variants are predicted to be more infectious and less lethal compared to the original spike protein. However, lineage B.1.351 (Beta variant) is predicted to be less infectious and more lethal, and lineage B.1.1.7 (Alpha variant) is predicted to have both higher infectivity and lethality, showing the potential of the virus to mutate towards different performance regimes. The relatively more recent lineage B.1.617.2 (Delta variant), although contains a few key spike mutations other than D614G, behaves quite similar to the single D614G mutation in both vibrational and predicted epidemiological aspects, which might explain its rapid circulation given the prevalence of D614G. This work may provide a tool to estimate the epidemiological effects of new variants, and offer a pathway to screen mutations against high threat levels. Moreover, the nanomechanical approach, as a novel tool to predict virus-cell interactions, may further open up the door towards better understanding other viruses.
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Affiliation(s)
- Yiwen Hu
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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7
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Kolel-Veetil MK, Kant A, Shenoy VB, Buehler MJ. SARS-CoV-2 Infection-Of Music and Mechanics of Its Spikes! A Perspective. ACS NANO 2022; 16:6949-6955. [PMID: 35512182 PMCID: PMC9092193 DOI: 10.1021/acsnano.1c11491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/26/2022] [Indexed: 05/11/2023]
Abstract
The COVID-19 pandemic has been inflicted upon humanity by the SARS-CoV-2 virus, the latest insidious incarnation of the coronaviruses group. While in its wake intense scientific research has produced breakthrough vaccines and cures, there still exists an immediate need to further understand the origin, mechanobiology and biochemistry, and destiny of this virus so that future pandemics arising from similar coronaviruses may be contained more effectively. In this Perspective, we discuss the various evidential findings of virus propagation and connect them to respective underpinning cellular biomechanical states leading to corresponding manifestations of the viral activity. We further propose avenues to tackle the virus, including from a "musical" vantage point, and contain its relentless strides that are currently afflicting the global populace.
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Affiliation(s)
- Manoj K. Kolel-Veetil
- Chemistry Division, Naval Research
Laboratory, Washington, D.C. 20375, United States
| | - Aayush Kant
- NSF Science and Technology Center for Engineering
Mechanobiology, University of Pennsylvania, Philadelphia,
Pennsylvania 19104, United States
| | - Vivek B. Shenoy
- NSF Science and Technology Center for Engineering
Mechanobiology, University of Pennsylvania, Philadelphia,
Pennsylvania 19104, United States
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM),
Massachusetts Institute of Technology, Cambridge,
Massachusetts 02139, United States
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8
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Wierzbicki T, Bai Y. Finite element modeling of alpha-helices and tropocollagen molecules with reference to the spike of SARS-CoV-2. Biophys J 2022; 121:2353-2370. [PMID: 35598047 PMCID: PMC9162829 DOI: 10.1016/j.bpj.2022.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/03/2022] [Accepted: 05/17/2022] [Indexed: 11/02/2022] Open
Abstract
The newly developed finite element modeling at the atomic scale was used to predict the static and dynamic response of the alpha-helix (AH) and tropocollagen (TC) protein fragments, the main building blocks of the spike of the SARS-CoV-2. The geometry and morphology of the spike's stalk and its connection to the viral envelope were determined from the combination of most recent Molecular Dynamics simulation and images of Cryo-Electron microscope. The stiffness parameters of the covalent bonds in the main chain of the helix were taken from the literature. The AH and TC were modeled using both beam elements (wire model) and shell elements (ribbon model) in finite element analysis to predict their mechanical properties under tension. The asymptotic stiffening features of AH and TC under tensile loading were revealed and compared with a new analytical solution. The mechanical stiffnesses under other loading conditions, including compression, torsion and bending were also predicted numerically and correlated with the results of the existing MD simulations and tests. The mode shapes and natural frequencies of the spike were predicted using the built FE model. The frequencies were shown to be within the safe range of 1-20 MHz routinely used for medical imaging and diagnosis by means of ultrasound. These results provide a solid theoretical basis for using ultrasound to study damaging coronavirus through transient and resonant vibration at large deformations.
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Affiliation(s)
- Tomasz Wierzbicki
- Impact and Crashworthiness Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuanli Bai
- Department of Mechanical and Aerospace of Engineering, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
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9
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Shahzad S, Willcox M. The Possible Role of Prion-Like Viral Protein Domains on the Emergence of Novel Viruses as SARS-CoV-2. J Mol Evol 2022; 90:227-230. [PMID: 35362781 PMCID: PMC8972983 DOI: 10.1007/s00239-022-10054-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/24/2022] [Indexed: 01/21/2023]
Abstract
Self-replicating proteins or prions deviate from the central dogma of replication. The discovery of prion-like domains in coronavirus SARS-CoV-2 suggests their possible role in viral evolution. Here, we have outlined the possible role of self-replicating protein-like domains in the emergence of novel viruses. Further studies are needed to understand the function of these viral self-replicating protein-like domains and whether they could be antiviral target(s) for the development of effective antiviral agents in the future.
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Affiliation(s)
- Shakeel Shahzad
- Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, NSW 2052 Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales Sydney, Sydney, NSW 2052 Australia
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10
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Guo K, Buehler MJ. Rapid prediction of protein natural frequencies using graph neural networks. DIGITAL DISCOVERY 2022; 1:277-285. [PMID: 35769204 PMCID: PMC9189858 DOI: 10.1039/d1dd00007a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022]
Abstract
Natural vibrational frequencies of proteins help to correlate functional shifts with sequence or geometric variations that lead to negligible changes in protein structures, such as point mutations related to disease lethality or medication effectiveness. Normal mode analysis is a well-known approach to accurately obtain protein natural frequencies. However, it is not feasible when high-resolution protein structures are not available or time consuming to obtain. Here we provide a machine learning model to directly predict protein frequencies from primary amino acid sequences and low-resolution structural features such as contact or distance maps. We utilize a graph neural network called principal neighborhood aggregation, trained with the structural graphs and normal mode frequencies of more than 34 000 proteins from the protein data bank. combining with existing contact/distance map prediction tools, this approach enables an end-to-end prediction of the frequency spectrum of a protein given its primary sequence. We present a computational framework based on graph neural networks (GNNs) to predict the natural frequencies of proteins from primary amino acid sequences and contact/distance maps.![]()
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Affiliation(s)
- Kai Guo
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-165, Cambridge, Massachusetts 02139, USA
- Institute of High Performance Computing, A*STAR, Singapore 138632, Singapore
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-165, Cambridge, Massachusetts 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Center for Materials Science and Engineering, 77 Massachusetts Ave, Cambridge, Massachusetts 02139, USA
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11
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Milazzo M, Anderson GI, Buehler MJ. Bioinspired translation of classical music into de novoprotein structures using deep learning and molecular modeling. BIOINSPIRATION & BIOMIMETICS 2021; 17:015001. [PMID: 34700310 DOI: 10.1088/1748-3190/ac338a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/26/2021] [Indexed: 05/25/2023]
Abstract
Architected biomaterials, as well as sound and music, are constructed from small building blocks that are assembled across time- and length-scales. Here we present a novel deep learning-enabled integrated algorithmic workflow to merge the two concepts for radical discovery ofde novoprotein materials, exploiting musical creativity as the foundation, and extrapolating through a recursive method to increase protein complexity by successively injecting protein chemistry into the process. Indeed, music is one of the few universal expressions that can create bridges between cultures, find associations between seemingly unrelated concepts, and can be used as a novel way to generate bio-inspired designs that derive functions from the imaginations of the creative mind. Earlier work has offered a pathway to convert proteins into sound, and sound into proteins. Here we build on this paradigm and translate a piece of classical music into matter. Based on Bach's Goldberg variations, we offer a series of case studies to convert the musical data imagined by the composer into protein design, and folded into a 3D structure using deep learning. The quest we seek to address is to identify semblances, or memories, or information content in such musical creation, that offers new insights into pattern relationships between distinct manifestations of information. Using basic local alignment search tool analysis, we find that several fragments of the new proteins display similarities to existing protein sequences found in proteobacteria among other organisms, especially in regions of low complexity and repetitive motifs. The resulting protein forms the basis for iterative musical composition, and an evolutionary paradigm that defines a variational pathway for melodic development, complementing conventional creative or mathematical methods. This paper broadens the concept of what is understood as bio-inspiration to include a broad array of systems created by humans, animals, or other natural mechanisms.
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Affiliation(s)
- Mario Milazzo
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States of America
| | - Grace I Anderson
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States of America
- Center for Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States of America
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States of America
- Center for Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States of America
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, United States of America
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12
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Modeling coronavirus spike protein dynamics: implications for immunogenicity and immune escape. Biophys J 2021; 120:5592-5618. [PMID: 34767789 PMCID: PMC8577870 DOI: 10.1016/j.bpj.2021.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/19/2021] [Accepted: 11/04/2021] [Indexed: 12/23/2022] Open
Abstract
The ongoing COVID-19 pandemic is a global public health emergency requiring urgent development of efficacious vaccines. While concentrated research efforts have focused primarily on antibody-based vaccines that neutralize SARS-CoV-2, and several first-generation vaccines have either been approved or received emergency use authorization, it is forecasted that COVID-19 will become an endemic disease requiring updated second-generation vaccines. The SARS-CoV-2 surface spike (S) glycoprotein represents a prime target for vaccine development because antibodies that block viral attachment and entry, i.e., neutralizing antibodies, bind almost exclusively to the receptor-binding domain. Here, we develop computational models for a large subset of S proteins associated with SARS-CoV-2, implemented through coarse-grained elastic network models and normal mode analysis. We then analyze local protein domain dynamics of the S protein systems and their thermal stability to characterize structural and dynamical variability among them. These results are compared against existing experimental data and used to elucidate the impact and mechanisms of SARS-CoV-2 S protein mutations and their associated antibody binding behavior. We construct a SARS-CoV-2 antigenic map and offer predictions about the neutralization capabilities of antibody and S mutant combinations based on protein dynamic signatures. We then compare SARS-CoV-2 S protein dynamics to SARS-CoV and MERS-CoV S proteins to investigate differing antibody binding and cellular fusion mechanisms that may explain the high transmissibility of SARS-CoV-2. The outbreaks associated with SARS-CoV, MERS-CoV, and SARS-CoV-2 over the last two decades suggest that the threat presented by coronaviruses is ever-changing and long term. Our results provide insights into the dynamics-driven mechanisms of immunogenicity associated with coronavirus S proteins and present a new, to our knowledge, approach to characterize and screen potential mutant candidates for immunogen design, as well as to characterize emerging natural variants that may escape vaccine-induced antibody responses.
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13
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Presas A, Valentin D, Deering J, Kampschulte M, Yu B, Grandfield K, Mele E, Biehl C, Krombach GA, Heiss C, Bosbach WA. Resonance vibration interventions in the femur: Experimental-numerical modelling approaches. J Mech Behav Biomed Mater 2021; 124:104850. [PMID: 34607300 DOI: 10.1016/j.jmbbm.2021.104850] [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: 04/21/2021] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 10/20/2022]
Abstract
MOTIVE External vibration excitation might be key to many novel non-surgical interventions for pathologies in the musculoskeletal system and in other parts of the human organism. Lack of understanding about vibration patterns, their controllability, and reproducibility are three limitations of ongoing research. This study establishes a bovine vibration model and animal model replacements for future research. METHODS We used biological samples (n=5) and one polyurethane sample of the bovine femur. Mechanical resonance was measured experimentally and analysed numerically by finite element method. MAIN RESULTS The experiments obtained 5 distinct mode shapes for the biological sample set, with standard deviation < 7.5%. Finite element analysis of the biological samples can replicate experimental mode shape deflection. The use of polyurethane changes resonance character but results are also good approximations of the biological samples. CONCLUSIONS A model of the bovine femur with consistent resonance behaviour is presented with alternatives (polyurethane and finite element analysis) that can serve in reducing the number of necessary biological samples. Future work will be to adapt results to human anatomy. Of clinical interest will be to influence bone pathologies such as post-surgical non-union, or bone functionality as part of haematopoiesis and endocrine secretion.
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Affiliation(s)
- Alexandre Presas
- Center for Industrial Diagnostics and Fluid Dynamics (CDIF), Polytechnic University of Catalonia (UPC), Spain
| | - David Valentin
- Center for Industrial Diagnostics and Fluid Dynamics (CDIF), Polytechnic University of Catalonia (UPC), Spain
| | - Joseph Deering
- Department of Materials Science and Engineering, McMaster University, Hamilton, ON, Canada
| | - Marian Kampschulte
- Experimental Radiology, Justus Liebig University of Giessen, Germany; Department of Diagnostic and Interventional, and Paediatric Radiology, University Hospital of Giessen, Germany
| | - Bosco Yu
- Department of Materials Science and Engineering, McMaster University, Hamilton, ON, Canada
| | - Kathryn Grandfield
- Department of Materials Science and Engineering, McMaster University, Hamilton, ON, Canada; School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada
| | - Elisa Mele
- Materials Department, Loughborough University, Loughborough, UK
| | - Christoph Biehl
- Experimental Trauma Surgery, Justus Liebig University of Giessen, Germany; Department of Trauma, Hand and Reconstructive Surgery, University Hospital of Giessen, Germany
| | - Gabriele A Krombach
- Experimental Radiology, Justus Liebig University of Giessen, Germany; Department of Diagnostic and Interventional, and Paediatric Radiology, University Hospital of Giessen, Germany
| | - Christian Heiss
- Experimental Trauma Surgery, Justus Liebig University of Giessen, Germany; Department of Trauma, Hand and Reconstructive Surgery, University Hospital of Giessen, Germany
| | - Wolfram A Bosbach
- Experimental Trauma Surgery, Justus Liebig University of Giessen, Germany; Department of Trauma, Hand and Reconstructive Surgery, University Hospital of Giessen, Germany.
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Milazzo M, Buehler MJ. Designing and fabricating materials from fire using sonification and deep learning. iScience 2021; 24:102873. [PMID: 34409268 PMCID: PMC8361214 DOI: 10.1016/j.isci.2021.102873] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/28/2021] [Accepted: 07/14/2021] [Indexed: 11/26/2022] Open
Abstract
Fire has fascinated humankind since the prehistoric era. Rooted in the interactions between sound and flames, here we report a method to use fire for a variety of purposes, including sonification, art, and the design and manufacturing nature-inspired materials. We present a method to sonify fire, thereby offering a translation from the silent nature of flames, to represent audible information and to generate de novo flame images. To realize material specimen derived from fire, we use the autoencoder to generate image stacks to yield continuous 3D geometries that are manufactured using 3D printing. This represents the first generation of nature-inspired materials from fire and can be a platform to be used for other natural phenomena in the quest for de novo architectures, geometries, and design ideas, thus creating additional directions in artistic and scientific research through the creative manipulation of data with structural similarities across fields.
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Affiliation(s)
- Mario Milazzo
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Rm. 1-165, Cambridge, MA 02139, USA
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Rm. 1-165, Cambridge, MA 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Center for Materials Science and Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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15
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Wierzbicki T, Li W, Liu Y, Zhu J. Effect of receptors on the resonant and transient harmonic vibrations of Coronavirus. JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS 2021; 150:104369. [PMID: 33623172 PMCID: PMC7890278 DOI: 10.1016/j.jmps.2021.104369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 05/06/2023]
Abstract
The paper is concerned with the vibration characteristics of the Coronavirus family. There are some 25-100 receptors, commonly called spikes protruding from the envelope shell of the virus. Spikes, resembling the shape of a hot air balloon, may have a total mass similar to the mass of the lipid bi-layer shell. The lipid proteins of the virus are treated as homogeneous elastic material and the problem is formulated as the interaction of thin elastic shell with discrete masses, modeled as short conical cross-sectional beams. The system is subjected to ultrasonic excitation. Using the methods of structural acoustics, it is shown that the scattered pressure is very small and the pressure on the viral shell is simply the incident pressure. The modal analysis is performed for a bare shell, a single spike, and the spike-decorated shell. The predicted vibration frequencies and modes are shown to compare well with the newly derived closed-form solutions for a single spike and existing analytical solutions for thin shells. The fully nonlinear dynamic simulation of the transient response revealed the true character of the complex interaction between local vibration of spikes and global vibration of the multi-degree-of-freedom system. It was shown that harmonic vibration at or below the lowest resonant modes can excite large amplitude vibration of spikes. The associated maximum principal strain in a spike can reach large values in a fraction of a millisecond. Implications for possible tearing off spikes from the shell are discussed. Another important result is that after a finite number of cycles, the shell buckles and collapses, developing internal contacts and folds with large curvatures and strains exceeding 10%. For the geometry and elastic properties of the SARS-CoV-2 virus, these effects are present in the range of frequencies close to the ones used for medical ultrasound diagnostics.
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Affiliation(s)
| | - Wei Li
- Department of Mechanical Engineering, MIT, United States
| | - Yuming Liu
- Department of Mechanical Engineering, MIT, United States
| | - Juner Zhu
- Department of Mechanical Engineering, MIT, United States
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16
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Poustforoosh A, Hashemipour H, Tüzün B, Pardakhty A, Mehrabani M, Nematollahi MH. Evaluation of potential anti-RNA-dependent RNA polymerase (RdRP) drugs against the newly emerged model of COVID-19 RdRP using computational methods. Biophys Chem 2021; 272:106564. [PMID: 33711743 PMCID: PMC7895701 DOI: 10.1016/j.bpc.2021.106564] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/19/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Despite all the efforts to treat COVID-19, no particular cure has been found for this virus. Since developing antiviral drugs is a time-consuming process, the most effective approach is to evaluate the approved and under investigation drugs using in silico methods. Among the different targets within the virus structure, as a vital component in the life cycle of coronaviruses, RNA-dependent RNA polymerase (RdRP) can be a critical target for antiviral drugs. The impact of the existence of RNA in the enzyme structure on the binding affinity of anti-RdRP drugs has not been investigated so far. METHODS In this study, the potential anti-RdRP effects of a variety of drugs from two databases (Zinc database and DrugBank) were evaluated using molecular docking. For this purpose, the newly emerged model of COVID-19 (RdRP) post-translocated catalytic complex (PDB ID: 7BZF) that consists of RNA was chosen as the target. RESULTS The results indicated that idarubicin (IDR), a member of the anthracycline antibiotic family, and fenoterol (FNT), a known beta-2 adrenergic agonist drug, tightly bind to the target enzyme and could be used as potential anti-RdRP inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These outcomes revealed that due to the ligand-protein interactions, the presence of RNA in this structure could remarkably affect the binding affinity of inhibitor compounds. CONCLUSION In silico approaches, such as molecular docking, could effectively address the problem of finding appropriate treatment for COVID-19. Our results showed that IDR and FNT have a significant affinity to the RdRP of SARS-CoV-2; therefore, these drugs are remarkable inhibitors of coronaviruses.
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Affiliation(s)
- Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hassan Hashemipour
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran; Chemical Engineering Department, Faculty of Engineering, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Burak Tüzün
- Department of Chemistry, Faculty of Science, Sivas Cumhuriyet University, Turkey
| | - Abbas Pardakhty
- Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehrnaz Mehrabani
- Physiology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hadi Nematollahi
- Herbal and Traditional Medicines Research Center, Kerman University of Medical Sciences, Kerman, Iran; Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of medical sciences, Kerman, Iran.
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