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Stern JA, Free TJ, Stern KL, Gardiner S, Dalley NA, Bundy BC, Price JL, Wingate D, Della Corte D. A probabilistic view of protein stability, conformational specificity, and design. Sci Rep 2023; 13:15493. [PMID: 37726313 PMCID: PMC10509192 DOI: 10.1038/s41598-023-42032-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Various approaches have used neural networks as probabilistic models for the design of protein sequences. These "inverse folding" models employ different objective functions, which come with trade-offs that have not been assessed in detail before. This study introduces probabilistic definitions of protein stability and conformational specificity and demonstrates the relationship between these chemical properties and the [Formula: see text] Boltzmann probability objective. This links the Boltzmann probability objective function to experimentally verifiable outcomes. We propose a novel sequence decoding algorithm, referred to as "BayesDesign", that leverages Bayes' Rule to maximize the [Formula: see text] objective instead of the [Formula: see text] objective common in inverse folding models. The efficacy of BayesDesign is evaluated in the context of two protein model systems, the NanoLuc enzyme and the WW structural motif. Both BayesDesign and the baseline ProteinMPNN algorithm increase the thermostability of NanoLuc and increase the conformational specificity of WW. The possible sources of error in the model are analyzed.
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Affiliation(s)
- Jacob A Stern
- Department of Computer Science, Brigham Young University, Provo, UT, USA
| | - Tyler J Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Kimberlee L Stern
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Spencer Gardiner
- Department of Physics and Astronomy, Brigham Young University, Provo, UT, USA
| | - Nicholas A Dalley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Joshua L Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - David Wingate
- Department of Computer Science, Brigham Young University, Provo, UT, USA
| | - Dennis Della Corte
- Department of Physics and Astronomy, Brigham Young University, Provo, UT, USA.
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Yang Y, Sun SH, Zou L, Wang B, Bian X, Zhu PY, Ren LK, Shi YG, Zhang N. Characterization of structural and functional properties of soybean 11S globulin during the renaturation after the guanidine hydrochloride denaturation. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sun F, Tao R, Liu Q, Wang H, Kong B. Effects of temperature and pH on the structure of a metalloprotease from Lactobacillus fermentum R6 isolated from Harbin dry sausages and molecular docking between protease and meat protein. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:5016-5027. [PMID: 33548144 DOI: 10.1002/jsfa.11146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/03/2021] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Microbial protease can interact with meat protein in fermented meat products at a certain pH and temperature. To investigate the effects of various pH values and temperatures on the structural characteristics of Lactobacillus fermentum R6 protease, which was isolated from Harbin dry sausages, spectroscopy techniques and molecular dynamics were utilized to evaluate structural changes. RESULTS The protease exhibited a stable spatial structure at pH 7 and 40 °C, and the extension of the protease structure was also promoted. Although the structure of the protease could be changed or destroyed by pH 8 and 70 °C, it was mainly determined by the changes of secondary and tertiary structures such as α-helix, β-sheet, β-turn and random coil. In addition, carbonyl vibration, -NH vibration, C-H stretching vibration and disulphide bonds were present in L. fermentum R6 protease under various pH and temperature conditions. Molecular docking showed that the protease can interact with myosin light chain, myosin heavy chain, actin and myoglobin. CONCLUSION The protease can maintain stable structure and interact with meat protein, which reflected certain application prospects in the fermentation of Harbin dry sausages. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Fangda Sun
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Ran Tao
- Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Qian Liu
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Hui Wang
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Baohua Kong
- College of Food Science, Northeast Agricultural University, Harbin, China
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Sun F, Wang H, Liu Q, Kong B, Chen Q. Effects of temperature and pH on the structure of a protease from Lactobacillus brevis R4 isolated from Harbin dry sausage and molecular docking of the protease to the meat proteins. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Sun F, Wang H, Wang H, Xia X, Kong B. Impacts of pH and temperature on the conformation of a protease from Pediococcus pentosaceus R1 isolated from Harbin dry sausage. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Wang W, Xi L, Xiong X, Li X, Zhang Q, Yang W, Du L. Insight into the structural stability of wild-type and histidine mutants in Pin1 by experimental and computational methods. Sci Rep 2019; 9:8413. [PMID: 31182777 PMCID: PMC6557836 DOI: 10.1038/s41598-019-44926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/28/2019] [Indexed: 01/21/2023] Open
Abstract
Pin1, a polypeptide proline isomerase parvulin, plays a key role in Alzheimer's disease (AD), common tumors and cancers. Two conservative histidine residues, His59 and His157, are important for maintaining the stability of the PPIase domain. Hence multiple spectral and computational techniques were performed to investigate the potential mechanism of two histidine residues. Thermal denaturation indicated that both residues His59 and His157 are not sensitive to the lower temperatures, while residue His59 is more sensitive to the higher temperatures than residue His157. Acidic denaturation suggested that influences of both residues His59 and His157 to acidic stability were the difference from Pin1-WT. ANS and RLS spectra hinted that there was no significant effect on hydrophobic change and aggregation by histidine mutations. The GndHCl-induced denaturation implied that residues His59 and His157 contributed the most to the chemical stability. MD simulations revealed that residues His59 and His157 mutations resulted in that the hydrogen bond network of the dual histidine motif was destroyed wholly. In summary, these histidine residues play an important role in maintaining the structural stability of the PPIase domain.
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Affiliation(s)
- Wang Wang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Lei Xi
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Xiuhong Xiong
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Xue Li
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Qingyan Zhang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Wentao Yang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Linfang Du
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China.
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The acidic pH-induced structural changes in apo-CP43 by spectral methodologies and molecular dynamics simulations. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.09.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Understanding the thermal stability of human serum proteins with the related near-infrared spectral variables selected by Monte Carlo-uninformative variable elimination. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.03.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Fan M, Cai W, Shao X. Investigating the Structural Change in Protein Aqueous Solution Using Temperature-Dependent Near-Infrared Spectroscopy and Continuous Wavelet Transform. APPLIED SPECTROSCOPY 2017; 71:472-479. [PMID: 27650983 DOI: 10.1177/0003702816664103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The circulatory protein, human serum albumin (HSA), is widely used as a model protein for the study of protein structure. In this work, the structures of human serum albumin in aqueous solutions are studied using temperature-dependent near-infrared (NIR) spectroscopy with the aid of continuous wavelet transform (CWT). Near-infrared spectra of human serum albumin solutions with different concentrations were measured over a temperature range of 30-85 ℃. Then, continuous wavelet transform was performed on the spectra to enhance the resolution. As a result of the resolution enhancement, spectral bands around 4361, 4521, 4600 and 4260 cm-1 were extracted from the overlapping low-resolution signals. The four bands can be assigned to the protein structures of α-helix, β-sheet, an intermediate state and side chains, respectively. The variations in intensity of the bands around 4361 and 4521 cm-1 with temperature show that the increase of temperature leads to the loss of α-helical structure but the formation of β-sheet, and the denaturation temperature of human serum albumin is about 55 ℃. The variation of the band around 4600 cm-1 indicates that the temperature-induced unfolding process of human serum albumin occurs through a stable intermediate state, and a significant change in the microenvironment of the side chains about 63 ℃ is observed from the variation of the band around 4260 cm-1. On the other hand, the transformed spectra in the region of 8000-5600 cm-1 provide an explicit evidence for the structural changes of water during the process of protein denaturation, and the unfolding process of HSA can be reflected by these changes.
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Affiliation(s)
- Mengli Fan
- 1 Research Center for Analytical Sciences, Nankai University, China
| | - Wensheng Cai
- 1 Research Center for Analytical Sciences, Nankai University, China
| | - Xueguang Shao
- 1 Research Center for Analytical Sciences, Nankai University, China
- 2 Tianjin Key Laboratory of Biosensing and Molecular Recognition, China
- 3 State Key Laboratory of Medicinal Chemical Biology, China
- 4 Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), China
- 5 College of Chemistry and Environmental Science, Kashgar University, China
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