1
|
Babbitt GA, Rajendran M, Lynch ML, Asare-Bediako R, Mouli LT, Ryan CJ, Srivastava H, Rynkiewicz P, Phadke K, Reed ML, Moore N, Ferran MC, Fokoue EP. ATOMDANCE: Kernel-based denoising and choreographic analysis for protein dynamic comparison. Biophys J 2024:S0006-3495(24)00204-2. [PMID: 38515299 DOI: 10.1016/j.bpj.2024.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/16/2023] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
Comparative methods in molecular evolution and structural biology rely heavily upon the site-wise analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from nanoscale nonrandom machine-like motions induced by evolutionarily conserved molecular interactions. Comparisons of molecular dynamics (MD) simulations conducted between homologous sites representative of different functional or mutational states can potentially identify local effects on binding interaction and protein evolution. In addition, comparisons of different (i.e., nonhomologous) sites within MD simulations could be employed to identify functional shifts in local time-coordinated dynamics indicative of logic gating within proteins. However, comparative MD analysis is challenged by the large fraction of protein motion caused by random thermal noise in the surrounding solvent. Therefore, properly denoised MD comparisons could reveal functional sites involving these machine-like dynamics with good accuracy. Here, we introduce ATOMDANCE, a user-interfaced suite of comparative machine learning-based denoising tools designed for identifying functional sites and the patterns of coordinated motion they can create within MD simulations. ATOMDANCE-maxDemon4.0 employs Gaussian kernel functions to compute site-wise maximum mean discrepancy between learned features of motion, thereby assessing denoised differences in the nonrandom motions between functional or evolutionary states (e.g., ligand bound versus unbound, wild-type versus mutant). ATOMDANCE-maxDemon4.0 also employs maximum mean discrepancy to analyze potential random amino acid replacements allowing for a site-wise test of neutral versus nonneutral evolution on the divergence of dynamic function in protein homologs. Finally, ATOMDANCE-Choreograph2.0 employs mixed-model analysis of variance and graph network to detect regions where time-synchronized shifts in dynamics occur. Here, we demonstrate ATOMDANCE's utility for identifying key sites involved in dynamic responses during functional binding interactions involving DNA, small-molecule drugs, and virus-host recognition, as well as understanding shifts in global and local site coordination occurring during allosteric activation of a pathogenic protease.
Collapse
Affiliation(s)
- Gregory A Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York.
| | - Madhusudan Rajendran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Miranda L Lynch
- Hauptmann Woodward Medical Research Institute, Buffalo, New York
| | - Richmond Asare-Bediako
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Leora T Mouli
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Cameron J Ryan
- McQuaid Jesuit High School Computer Club, Rochester, New York
| | | | - Patrick Rynkiewicz
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Kavya Phadke
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Makayla L Reed
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Nadia Moore
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Maureen C Ferran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Ernest P Fokoue
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York.
| |
Collapse
|
2
|
Rajendran M, Babbitt GA. Persistent cross-species SARS-CoV-2 variant infectivity predicted via comparative molecular dynamics simulation. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220600. [PMID: 36340517 PMCID: PMC9626255 DOI: 10.1098/rsos.220600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Widespread human transmission of SARS-CoV-2 highlights the substantial public health, economic and societal consequences of virus spillover from wildlife and also presents a repeated risk of reverse spillovers back to naive wildlife populations. We employ comparative statistical analyses of a large set of short-term molecular dynamic (MD) simulations to investigate the potential human-to-bat (genus Rhinolophus) cross-species infectivity allowed by the binding of SARS-CoV-2 receptor-binding domain (RBD) to angiotensin-converting enzyme 2 (ACE2) across the bat progenitor strain and emerging human strain variants of concern (VOC). We statistically compare the dampening of atom motion across protein sites upon the formation of the RBD/ACE2 binding interface using various bat versus human target receptors (i.e. bACE2 and hACE2). We report that while the bat progenitor viral strain RaTG13 shows some pre-adaption binding to hACE2, it also exhibits stronger affinity to bACE2. While early emergent human strains and later VOCs exhibit robust binding to both hACE2 and bACE2, the delta and omicron variants exhibit evolutionary adaption of binding to hACE2. However, we conclude there is a still significant risk of mammalian cross-species infectivity of human VOCs during upcoming waves of infection as COVID-19 transitions from a pandemic to endemic status.
Collapse
Affiliation(s)
- Madhusudan Rajendran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Gregory A. Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| |
Collapse
|
3
|
Rajendran M, Ferran MC, Babbitt GA. Identifying vaccine escape sites via statistical comparisons of short-term molecular dynamics. BIOPHYSICAL REPORTS 2022; 2:100056. [PMID: 35403093 PMCID: PMC8978532 DOI: 10.1016/j.bpr.2022.100056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/31/2022] [Indexed: 01/08/2023]
Abstract
The identification of viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. We describe a molecular dynamics (MD)-based approach that goes beyond contact mapping, scales well to a desktop computer with a modern graphics processor, and enables the user to identify functional protein sites that are prone to vaccine escape in a viral antigen. We first implement our MD pipeline to employ site-wise calculation of Kullback-Leibler divergence in atom fluctuation over replicate sets of short-term MD production runs thus enabling a statistical comparison of the rapid motion of influenza hemagglutinin (HA) in both the presence and absence of three well-known neutralizing antibodies. Using this simple comparative method applied to motions of viral proteins, we successfully identified in silico all previously empirically confirmed sites of escape in influenza HA, predetermined via selection experiments and neutralization assays. Upon the validation of our computational approach, we then surveyed potential hotspot residues in the receptor binding domain of the SARS-CoV-2 virus in the presence of COVOX-222 and S2H97 antibodies. We identified many single sites in the antigen-antibody interface that are similarly prone to potential antibody escape and that match many of the known sites of mutations arising in the SARS-CoV-2 variants of concern. In the Omicron variant, we find only minimal adaptive evolutionary shifts in the functional binding profiles of both antibodies. In summary, we provide an inexpensive and accurate computational method to monitor hotspots of functional evolution in antibody binding footprints.
Collapse
|
4
|
Babbitt GA, Fokoue EP, Srivastava HR, Callahan B, Rajendran M. Statistical machine learning for comparative protein dynamics with the DROIDS/maxDemon software pipeline. STAR Protoc 2022; 3:101194. [PMID: 35252883 PMCID: PMC8888980 DOI: 10.1016/j.xpro.2022.101194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative analysis of protein structure or sequence alignments often ignores the protein dynamics and function. We offer a graphical user interface to a computing pipeline, complete with molecular visualization, enabling the biophysical simulation and statistical comparison of two-state functional protein dynamics (i.e., single unbound state vs. complex with a ligand, DNA, or protein). We utilize multi-agent machine learning classifiers to identify functionally conserved dynamic motions and compare them in genetic or drug-class variants. For complete details on the use and execution of this profile, please refer to Babbitt et al. (2020b, 2020a, 2018) and Rynkiewicz et al. (2021). A pipeline for the site-wise statistical comparison of molecular dynamics Analyzes mutational or functional changes in protein dynamics Utilizes machine learning to identify regions of conserved dynamics Utilizes information theoretics to identify site of coordinated dynamics
Collapse
Affiliation(s)
- Gregory A. Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
- Corresponding author
| | - Ernest P. Fokoue
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Harsh R. Srivastava
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Breanna Callahan
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Madhusudan Rajendran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| |
Collapse
|
5
|
Comparison of the Performance of the PanBio COVID-19 Antigen Test in SARS-CoV-2 B.1.1.7 (Alpha) Variants versus non-B.1.1.7 Variants. Microbiol Spectr 2021; 9:e0088421. [PMID: 34817226 PMCID: PMC8612141 DOI: 10.1128/spectrum.00884-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study evaluates the performance of the PanBio COVID-19 antigen (Ag) test as part of a hospital infection control policy. Hospital staff was encouraged to get tested for COVID-19 when presenting with SARS-CoV-2-related symptoms. In a period of approximately 5 months, a steady decline in the performance of the Ag test was noted, epidemiologically coinciding with the rise of the SARS-CoV-2 B.1.1.7 (alpha) variant of concern (VOC) in the Netherlands. This led to the hypothesis that the diagnostic performance of the PanBio COVID-19 Ag test was influenced by the infecting viral variant. The results show a significantly lower sensitivity of the PanBio COVID-19 Ag test in persons infected with the B.1.1.7 (alpha) variant of SARS-CoV-2 in comparison with that in persons infected with non-B.1.1.7 variants, also after adjustment for viral load. IMPORTANCE Antigen tests for COVID-19 are widely used for rapid identification of COVID-19 cases, for example, for access to schools, festivals, and travel. There are several FDA- and CE-cleared tests on the market. Their performance has been evaluated mainly on the basis of infections by the classical variant of the causing virus, SARS-CoV-2. This paper provides evidence that the performance of one of the most widely used antigen tests detects significantly fewer cases of COVID-19 by the alpha variant than by the classical variants of SARS-CoV-2. This means that the role of antigen tests needs to be reevaluated in regions where other variants of SARS-CoV-2 predominate.
Collapse
|