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Yang X, Mao Z, Huang J, Wang R, Dong H, Zhang Y, Ma H. Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments. Synth Syst Biotechnol 2023; 8:597-605. [PMID: 37743907 PMCID: PMC10514394 DOI: 10.1016/j.synbio.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/12/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Metabolic network models have become increasingly precise and accurate as the most widespread and practical digital representations of living cells. The prediction functions were significantly expanded by integrating cellular resources and abiotic constraints in recent years. However, if unreasonable modeling methods were adopted due to a lack of consideration of biological knowledge, the conflicts between stoichiometric and other constraints, such as thermodynamic feasibility and enzyme resource availability, would lead to distorted predictions. In this work, we investigated a prediction anomaly of EcoETM, a constraints-based metabolic network model, and introduced the idea of enzyme compartmentalization into the analysis process. Through rational combination of reactions, we avoid the false prediction of pathway feasibility caused by the unrealistic assumption of free intermediate metabolites. This allowed us to correct the pathway structures of l-serine and l-tryptophan. A specific analysis explains the application method of the EcoETM-like model and demonstrates its potential and value in correcting the prediction results in pathway structure by resolving the conflict between different constraints and incorporating the evolved roles of enzymes as reaction compartments. Notably, this work also reveals the trade-off between product yield and thermodynamic feasibility. Our work is of great value for the structural improvement of constraints-based models.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhitao Mao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jianfeng Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Ruoyu Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Huaming Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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2
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Wappett D, Goerigk L. Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set. J Chem Theory Comput 2023; 19:8365-8383. [PMID: 37943578 PMCID: PMC10688432 DOI: 10.1021/acs.jctc.3c00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.
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Affiliation(s)
- Dominique
A. Wappett
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
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3
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Gruss I, Twardowski J, Samsel-Czekała M, Beznosiuk J, Wandzel C, Twardowska K, Wiglusz RJ. The isothermal Boltzmann-Gibbs entropy reduction affects survival of the fruit fly Drosophila melanogaster. Sci Rep 2023; 13:14166. [PMID: 37644276 PMCID: PMC10465501 DOI: 10.1038/s41598-023-41482-x] [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: 05/10/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023] Open
Abstract
To the best of our knowledge, this is the first experimental evidence of the effect of isothermal changes in entropy on a living organism. In greater detail, the effect of the reduction of the total Boltzmann-Gibbs entropy (S) of the aquatic environment on the survival rate and body mass of the fruit fly Drosophila melanogaster was investigated. The tests were carried out in standard thermodynamic states at room temperature of 296.15 K and ambient atmospheric pressure of 1 bar. Two variants of entropy reduction (ΔS) were tested for ΔS = 28.49 and 51.14 J K-1 mol-1 compared to the blind and control samples. The entropy level was experimentally changed, using the quantum system for isothermal entropy reduction. This system is based on quantum bound entanglement of phonons and the phenomenon of phonon resonance (interference of phonon modes) in condensed matter (Silicon dioxide (SiO2) and single crystals of Silicon (Si0), Aluminum (Al0) plates ("chips"), glass, and water). All studied organisms were of the same age (1 day). Mortality was observed daily until the natural death of the organisms. The investigations showed that changes in the Boltzmann-Gibbs entropy affected the survival and body mass of the fruit flies. On the one hand, the reduction in entropy under isothermal conditions in the aquatic environment for ΔS = 28.49 J K-1 mol-1 resulted in an extension of the lifespan and an increase in the body mass of female fruit flies. On the other hand, the almost twofold reduction in this entropy for ΔS = 51.14 J K-1 mol-1 shortened the lives of the males. Thus, the lifespan and body mass of flies turned out to be a specific reaction of metabolism related to changes in the entropy of the aquatic environment.
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Affiliation(s)
- Iwona Gruss
- Department of Plant Protection, Wroclaw University of Environmental and Life Sciences, Grunwaldzki Sq. 24a, 50363, Wroclaw, Poland.
| | - Jacek Twardowski
- Department of Plant Protection, Wroclaw University of Environmental and Life Sciences, Grunwaldzki Sq. 24a, 50363, Wroclaw, Poland
| | - Małgorzata Samsel-Czekała
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okolna 2, 50422, Wroclaw, Poland
| | - Jarosław Beznosiuk
- PER Poland S.A, Ul. Zygmunta Starego 9, 44100, Gliwice, Poland
- PER Switzerland AG, Landstrasse 151, 9494, Schaan, Liechtenstein
| | - Czesław Wandzel
- PER Poland S.A, Ul. Zygmunta Starego 9, 44100, Gliwice, Poland
| | - Kamila Twardowska
- Department of Plant Protection, Wroclaw University of Environmental and Life Sciences, Grunwaldzki Sq. 24a, 50363, Wroclaw, Poland
| | - Rafal J Wiglusz
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okolna 2, 50422, Wroclaw, Poland.
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4
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McNaughton AD, Joshi RP, Knutson CR, Fnu A, Luebke KJ, Malerich JP, Madrid PB, Kumar N. Machine Learning Models for Predicting Molecular UV-Vis Spectra with Quantum Mechanical Properties. J Chem Inf Model 2023; 63:1462-1471. [PMID: 36847578 DOI: 10.1021/acs.jcim.2c01662] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Accurate understanding of ultraviolet-visible (UV-vis) spectra is critical for the high-throughput synthesis of compounds for drug discovery. Experimentally determining UV-vis spectra can become expensive when dealing with a large quantity of novel compounds. This provides us an opportunity to drive computational advances in molecular property predictions using quantum mechanics and machine learning methods. In this work, we use both quantum mechanically (QM) predicted and experimentally measured UV-vis spectra as input to devise four different machine learning architectures, UVvis-SchNet, UVvis-DTNN, UVvis-Transformer, and UVvis-MPNN, and assess the performance of each method. We find that the UVvis-MPNN model outperforms the other models when using optimized 3D coordinates and QM predicted spectra as input features. This model has the highest performance for predicting UV-vis spectra with a training RMSE of 0.06 and validation RMSE of 0.08. Most importantly, our model can be used for the challenging task of predicting differences in the UV-vis spectral signatures of regioisomers.
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Affiliation(s)
- Andrew D McNaughton
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rajendra P Joshi
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carter R Knutson
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Anubhav Fnu
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kevin J Luebke
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jeremiah P Malerich
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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5
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faiad naief M, Mishaal Mohammed A, Khalaf YH. Kinetic and thermodynamic study of ALP enzyme in the presence and absence MWCNTs and Pt-NPs nanocomposites. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
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6
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Armaković S, Armaković SJ. Atomistica.online – web application for generating input files for ORCA molecular modelling package made with the Anvil platform. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2126865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Novi Sad, Serbia
- Association for the International Development of Academic and Scientific Collaboration, Novi Sad, Serbia
| | - Sanja J. Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Novi Sad, Serbia
- Association for the International Development of Academic and Scientific Collaboration, Novi Sad, Serbia
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7
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McNaughton AD, Bredeweg EL, Manzer J, Zucker J, Munoz Munoz N, Burnet MC, Nakayasu ES, Pomraning KR, Merkley ED, Dai Z, Chrisler WB, Baker SE, St. John PC, Kumar N. Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling. ACS Synth Biol 2021; 10:2968-2981. [PMID: 34636549 DOI: 10.1021/acssynbio.1c00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Optimizing the metabolism of microbial cell factories for yields and titers is a critical step for economically viable production of bioproducts and biofuels. In this process, tuning the expression of individual enzymes to obtain the desired pathway flux is a challenging step, in which data from separate multiomics techniques must be integrated with existing biological knowledge to determine where changes should be made. Following a design-build-test-learn strategy, building on recent advances in Bayesian metabolic control analysis, we identify key enzymes in the oleaginous yeast Yarrowia lipolytica that correlate with the production of itaconate by integrating a metabolic model with multiomics measurements. To this extent, we quantify the uncertainty for a variety of key parameters, known as flux control coefficients (FCCs), needed to improve the bioproduction of target metabolites and statistically obtain key correlations between the measured enzymes and boundary flux. Based on the top five significant FCCs and five correlated enzymes, our results show phosphoglycerate mutase, acetyl-CoA synthetase (ACSm), carbonic anhydrase (HCO3E), pyrophosphatase (PPAm), and homoserine dehydrogenase (HSDxi) enzymes in rate-limiting reactions that can lead to increased itaconic acid production.
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Affiliation(s)
- Andrew D. McNaughton
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin L. Bredeweg
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - James Manzer
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jeremy Zucker
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Nathalie Munoz Munoz
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Meagan C. Burnet
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ernesto S. Nakayasu
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kyle R. Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric D. Merkley
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ziyu Dai
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William B. Chrisler
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Scott E. Baker
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Neeraj Kumar
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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8
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Joshi RP, Kumar N. Artificial Intelligence for Autonomous Molecular Design: A Perspective. Molecules 2021; 26:6761. [PMID: 34833853 PMCID: PMC8619999 DOI: 10.3390/molecules26226761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/23/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022] Open
Abstract
Domain-aware artificial intelligence has been increasingly adopted in recent years to expedite molecular design in various applications, including drug design and discovery. Recent advances in areas such as physics-informed machine learning and reasoning, software engineering, high-end hardware development, and computing infrastructures are providing opportunities to build scalable and explainable AI molecular discovery systems. This could improve a design hypothesis through feedback analysis, data integration that can provide a basis for the introduction of end-to-end automation for compound discovery and optimization, and enable more intelligent searches of chemical space. Several state-of-the-art ML architectures are predominantly and independently used for predicting the properties of small molecules, their high throughput synthesis, and screening, iteratively identifying and optimizing lead therapeutic candidates. However, such deep learning and ML approaches also raise considerable conceptual, technical, scalability, and end-to-end error quantification challenges, as well as skepticism about the current AI hype to build automated tools. To this end, synergistically and intelligently using these individual components along with robust quantum physics-based molecular representation and data generation tools in a closed-loop holds enormous promise for accelerated therapeutic design to critically analyze the opportunities and challenges for their more widespread application. This article aims to identify the most recent technology and breakthrough achieved by each of the components and discusses how such autonomous AI and ML workflows can be integrated to radically accelerate the protein target or disease model-based probe design that can be iteratively validated experimentally. Taken together, this could significantly reduce the timeline for end-to-end therapeutic discovery and optimization upon the arrival of any novel zoonotic transmission event. Our article serves as a guide for medicinal, computational chemistry and biology, analytical chemistry, and the ML community to practice autonomous molecular design in precision medicine and drug discovery.
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Affiliation(s)
| | - Neeraj Kumar
- Computational Biology Group, Biological Science Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA;
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