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Guo Q, Dan M, Zheng Y, Zhao G, Wang D. Construction and characterization of a novel fusion alginate lyase with endolytic and exolytic cleavage activity for industrial preparation of alginate oligosaccharides. Food Chem 2024; 453:139695. [PMID: 38788651 DOI: 10.1016/j.foodchem.2024.139695] [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: 01/26/2024] [Revised: 04/28/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Alginate lyases with high activity and good thermostability are lacking for the preparation of alginate oligosaccharides (AOS) with various biological activities. We constructed a fusion alginate lyase with both endo-and exo-activities. AlyRm6A-Zu7 was successfully constructed by connecting the highly thermostable AlyRm6A to a new exotype lyase, AlyZu7. The fusion enzyme exhibited high catalytic activity and thermostability. It transformed sodium alginate into oligosaccharides with degrees of polymerization (DP) of 2-4 while producing 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH). The maximum reducing sugar, AOS, and DP1 + DEH yields were 75 %, 45 %, and 40 %, respectively. Molecular docking confirmed the formation of a stable complex between the substrate and AlyRm6A-Zu7. Protein interactions increased the thermostability of AlyZu7. This work provides new insights into the industrial formation of AOS and monosaccharide DEH using thermally stable fusion enzymes, which has a positive effect in the fields of functional oligosaccharide production and biofuel formation.
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Affiliation(s)
- Qing Guo
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Meiling Dan
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuting Zheng
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Guohua Zhao
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Damao Wang
- College of Food Science, Southwest University, Chongqing 400715, China; Yibin Academy of Southwest University, Yibin, Sichuan 644000, China.
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2
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Rodella C, Lazaridi S, Lemmin T. TemBERTure: advancing protein thermostability prediction with deep learning and attention mechanisms. BIOINFORMATICS ADVANCES 2024; 4:vbae103. [PMID: 39040220 PMCID: PMC11262459 DOI: 10.1093/bioadv/vbae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/14/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Motivation Understanding protein thermostability is essential for numerous biotechnological applications, but traditional experimental methods are time-consuming, expensive, and error-prone. Recently, deep learning (DL) techniques from natural language processing (NLP) was extended to the field of biology, since the primary sequence of proteins can be viewed as a string of amino acids that follow a physicochemical grammar. Results In this study, we developed TemBERTure, a DL framework that predicts thermostability class and melting temperature from protein sequences. Our findings emphasize the importance of data diversity for training robust models, especially by including sequences from a wider range of organisms. Additionally, we suggest using attention scores from Deep Learning models to gain deeper insights into protein thermostability. Analyzing these scores in conjunction with the 3D protein structure can enhance understanding of the complex interactions among amino acid properties, their positioning, and the surrounding microenvironment. By addressing the limitations of current prediction methods and introducing new exploration avenues, this research paves the way for more accurate and informative protein thermostability predictions, ultimately accelerating advancements in protein engineering. Availability and implementation TemBERTure model and the data are available at: https://github.com/ibmm-unibe-ch/TemBERTure.
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Affiliation(s)
- Chiara Rodella
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern CH-3012, Switzerland
| | - Symela Lazaridi
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern CH-3012, Switzerland
| | - Thomas Lemmin
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
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Sadaqat B, Dar MA, Sha C, Abomohra A, Shao W, Yong YC. Thermophilic β-mannanases from bacteria: production, resources, structural features and bioengineering strategies. World J Microbiol Biotechnol 2024; 40:130. [PMID: 38460032 DOI: 10.1007/s11274-024-03912-4] [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: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 03/11/2024]
Abstract
β-mannanases are pivotal enzymes that cleave the mannan backbone to release short chain mannooligosaccharides, which have tremendous biotechnological applications including food/feed, prebiotics and biofuel production. Due to the high temperature conditions in many industrial applications, thermophilic mannanases seem to have great potential to overcome the thermal impediments. Thus, structural analysis of thermostable β-mannanases is extremely important, as it could open up new avenues for genetic engineering, and protein engineering of these enzymes with enhanced properties and catalytic efficiencies. Under this scope, the present review provides a state-of-the-art discussion on the thermophilic β-mannanases from bacterial origin, their production, engineering and structural characterization. It covers broad insights into various molecular biology techniques such as gene mutagenesis, heterologous gene expression, and protein engineering, that are employed to improve the catalytic efficiency and thermostability of bacterial mannanases for potential industrial applications. Further, the bottlenecks associated with mannanase production and process optimization are also discussed. Finally, future research related to bioengineering of mannanases with novel protein expression systems for commercial applications are also elaborated.
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Affiliation(s)
- Beenish Sadaqat
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 22100, Lund, Sweden
| | - Mudasir A Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Chong Sha
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Abdelfatah Abomohra
- Aquatic Ecophysiology and Phycology, Department of Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, 22609, Germany
| | - Weilan Shao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
| | - Yang-Chun Yong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
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Benrezkallah D. Molecular dynamics simulations at high temperatures of the Aeropyrum pernix L7Ae thermostable protein: Insight into the unfolding pathway. J Mol Graph Model 2024; 127:108700. [PMID: 38183846 DOI: 10.1016/j.jmgm.2023.108700] [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: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
Most life forms on earth live at temperatures below 50 °C. Within these organisms are proteins that form the three-dimensional structures essential to their biological activity and function. However, some thermophilic life forms can resist higher temperatures and have corresponding adaptations to preserve protein function at these high temperatures. Among the structural factors responsible for this resistance of thermophilic proteins to high temperatures is the presence of additional hydrogen bonds in the thermophilic proteins, which means that the structure of the protein is more resistant to unfolding. Similarly, thermostable proteins are rich in structure-stabilizing salt bridges and/or disulfide bridges. In this context, we perform multiple replica molecular dynamics simulations at different temperatures on the Aeropyrum pernix (L7Ae) protein (from the crenarchaeal species A. pernix), known for its high melting temperature, and this in the aim to elucidate the structural factors responsible for its high thermostability. The results reveal that between the most sensitive regions of the protein to the increase of temperature are the loops L1, and L5, which surround the hydrophobic core region of the protein, besides the loop L9, and the C-terminal α5 region. This latter is the longer alpha helix of the protein secondary structure motifs and it is the first to be denaturated at 450 K, while the rest of the protein secondary structure motifs at this temperature were intact. The mechanism of unfolding that follows this protein at 550 K is similar to other thermophile proteins found in literature, with the opening of the loops that surround the hydrophobic core of the protein. So, the latter is completely exposed to the solvent, and partially denatured. The total denaturation process of the protein takes an average time of 40 ns to be achieved. Our investigation also shows that all the calculated salt bridges, with distances less than or equal to 6 A°, are on the periphery part of the protein, exposed to the solvent. However, the hydrophobic core of the protein is not involved in the formation of salt bridges, but rather with formation of some important hydrogen bondings that still persist even at 450 K. So, optimizing hydrogen bonding, near or within the core region, at high temperatures is a strategy that follows this thermostable protein to protect its hydrophobic core from denaturation, and ensure the thermal stability of the protein.
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Affiliation(s)
- Djamila Benrezkallah
- Department of Basic Teachings in Sciences and Technologies (EBST), Faculty of Technology, Djillali Liabes University, Ben M'Hidi BP 89, Sidi Bel Abbes 22000, Algeria; LCPM Laboratory, Chemistry Department, Faculty of Exact and Applied Sciences, University Oran 1 Ahmed Ben Bella, El Mnaouer BP 1524, Oran 31000, Algeria.
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Xiang X, Gao J, Ding Y. DeepPPThermo: A Deep Learning Framework for Predicting Protein Thermostability Combining Protein-Level and Amino Acid-Level Features. J Comput Biol 2024; 31:147-160. [PMID: 38100126 DOI: 10.1089/cmb.2023.0097] [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] [Indexed: 02/15/2024] Open
Abstract
Using wet experimental methods to discover new thermophilic proteins or improve protein thermostability is time-consuming and expensive. Machine learning methods have shown powerful performance in the study of protein thermostability in recent years. However, how to make full use of multiview sequence information to predict thermostability effectively is still a challenge. In this study, we proposed a deep learning-based classifier named DeepPPThermo that fuses features of classical sequence features and deep learning representation features for classifying thermophilic and mesophilic proteins. In this model, deep neural network (DNN) and bi-long short-term memory (Bi-LSTM) are used to mine hidden features. Furthermore, local attention and global attention mechanisms give different importance to multiview features. The fused features are fed to a fully connected network classifier to distinguish thermophilic and mesophilic proteins. Our model is comprehensively compared with advanced machine learning algorithms and deep learning algorithms, proving that our model performs better. We further compare the effects of removing different features on the classification results, demonstrating the importance of each feature and the robustness of the model. Our DeepPPThermo model can be further used to explore protein diversity, identify new thermophilic proteins, and guide directed mutations of mesophilic proteins.
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Affiliation(s)
- Xiaoyang Xiang
- School of Science, Jiangnan University, Wuxi, P. R. China
| | - Jiaxuan Gao
- School of Science, Jiangnan University, Wuxi, P. R. China
| | - Yanrui Ding
- School of Science, Jiangnan University, Wuxi, P. R. China
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Wan H, Zhang Y, Huang S. Prediction of thermophilic protein using 2-D general series correlation pseudo amino acid features. Methods 2023; 218:141-148. [PMID: 37604248 DOI: 10.1016/j.ymeth.2023.08.012] [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: 05/03/2023] [Revised: 07/08/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023] Open
Abstract
The demand for thermophilic protein has been increasing in protein engineering recently. Many machine-learning methods for identifying thermophilic proteins have emerged during this period. However, most machine learning-based thermophilic protein identification studies have only focused on accuracy. The relationship between the features' meaning and the proteins' physicochemical properties has yet to be studied in depth. In this article, we focused on the relationship between the features and the thermal stability of thermophilic proteins. This method used 2-D general series correlation pseudo amino acid (SC-PseAAC-General) features and realized accuracy of 82.76% using the J48 classifier. In addition, this research found the presence of higher frequencies of glutamic acid in thermophilic proteins, which help thermophilic proteins maintain their thermal stability by forming hydrogen bonds and salt bridges that prevent denaturation at high temperatures.
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Affiliation(s)
- Hao Wan
- College of Life Science, Qingdao University, Qingdao 266071, China.
| | - Yanan Zhang
- College of Life Science, Qingdao University, Qingdao 266071, China
| | - Shibo Huang
- Beidahuang Industry Group General Hospital, Harbin 150001, China
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Che Hussian CHA, Leong WY. Thermostable enzyme research advances: a bibliometric analysis. J Genet Eng Biotechnol 2023; 21:37. [PMID: 36971917 PMCID: PMC10043094 DOI: 10.1186/s43141-023-00494-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/18/2023] [Indexed: 03/29/2023]
Abstract
Thermostable enzymes are enzymes that can withstand elevated temperatures as high as 50 °C without altering their structure or distinctive features. The potential of thermostable enzymes to increase the conversion rate at high temperature has been identified as a key factor in enhancing the efficiency of industrial operations. Performing procedures at higher temperatures with thermostable enzymes minimises the risk of microbial contamination, which is one of the most significant benefits. In addition, it helps reduce substrate viscosity, improve transfer speeds, and increase solubility during reaction operations. Thermostable enzymes offer enormous industrial potential as biocatalysts, especially cellulase and xylanase, which have garnered considerable amount of interest for biodegradation and biofuel applications. As the usage of enzymes becomes more common, a range of performance-enhancing applications are being explored. This article offers a bibliometric evaluation of thermostable enzymes. Scopus databases were searched for scientific articles. The findings indicated that thermostable enzymes are widely employed in biodegradation as well as in biofuel and biomass production. Japan, the United States, China, and India, as along with the institutions affiliated with these nations, stand out as the academically most productive in the field of thermostable enzymes. This study's analysis exposed a vast number of published papers that demonstrate the industrial potential of thermostable enzymes. These results highlight the significance of thermostable enzyme research for a variety of applications.
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Affiliation(s)
| | - Wai Yie Leong
- INTI International University & Colleges, Nilai, Negeri Sembilan, Malaysia
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McGuire BE, Nano FE. Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains. BMC Genomics 2023; 24:154. [PMID: 36973666 PMCID: PMC10044804 DOI: 10.1186/s12864-023-09266-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND High temperatures cause a suite of problems for cells, including protein unfolding and aggregation; increased membrane fluidity; and changes in DNA supercoiling, RNA stability, transcription and translation. Consequently, enhanced thermotolerance can evolve through an unknown number of genetic mechanisms even in the simple model bacterium Escherichia coli. To date, each E. coli study exploring this question resulted in a different set of mutations. To understand the changes that can arise when an organism evolves to grow at higher temperatures, we sequenced and analyzed two previously described E. coli strains, BM28 and BM28 ΔlysU, that have been laboratory adapted to the highest E. coli growth temperature reported to date. RESULTS We found three large deletions in the BM28 and BM28 ΔlysU strains of 123, 15 and 8.5 kb in length and an expansion of IS10 elements. We found that BM28 and BM28 ΔlysU have considerably different genomes, suggesting that the BM28 culture that gave rise to BM28 and BM28 ΔlysU was a mixed population of genetically different cells. Consistent with published findings of high GroESL expression in BM28, we found that BM28 inexplicitly carries the groESL bearing plasmid pOF39 that was maintained simply by high-temperature selection pressure. We identified over 200 smaller insertions, deletions, single nucleotide polymorphisms and other mutations, including changes in master regulators such as the RNA polymerase and the transcriptional termination factor Rho. Importantly, this genome analysis demonstrates that the commonly cited findings that LysU plays a crucial role in thermotolerance and that GroESL hyper-expression is brought about by chromosomal mutations are based on a previous misinterpretation of the genotype of BM28. CONCLUSIONS This whole-genome sequencing study describes genetically distinct mechanisms of thermotolerance evolution from those found in other heat-evolved E. coli strains. Studying adaptive laboratory evolution to heat in simple model organisms is important in the context of climate change. It is important to better understand genetic mechanisms of enhancing thermotolerance in bacteria and other organisms, both in terms of optimizing laboratory evolution methods for various organisms and in terms of potential genetic engineering of organisms most at risk or most important to our societies and ecosystems.
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Affiliation(s)
- Bailey E McGuire
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C, Canada.
| | - Francis E Nano
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C, Canada
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Kumar S, Duggineni VK, Singhania V, Misra SP, Deshpande PA. Unravelling and Quantifying the Biophysical– Biochemical Descriptors Governing Protein Thermostability by Machine Learning. ADVANCED THEORY AND SIMULATIONS 2023. [DOI: 10.1002/adts.202200703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Shashi Kumar
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Vinay Kumar Duggineni
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Vibhuti Singhania
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Swayam Prabha Misra
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
| | - Parag A. Deshpande
- Quantum and Molecular Engineering Laboratory Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur 721302 India
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Rabbani G, Ahmad E, Ahmad A, Khan RH. Structural features, temperature adaptation and industrial applications of microbial lipases from psychrophilic, mesophilic and thermophilic origins. Int J Biol Macromol 2023; 225:822-839. [PMID: 36402388 DOI: 10.1016/j.ijbiomac.2022.11.146] [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: 06/10/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Microbial lipases are very prominent biocatalysts because of their ability to catalyze a wide variety of reactions in aqueous and non-aqueous media. Here microbial lipases from different origins (psychrophiles, mesophiles, and thermophiles) have been reviewed. This review emphasizes an update of structural diversity in temperature adaptation and industrial applications, of psychrophilic, mesophilic, and thermophilic lipases. The microbial origins of lipases are logically dynamic, proficient, and also have an extensive range of industrial uses with the manufacturing of altered molecules. It is therefore of interest to understand the molecular mechanisms of adaptation to temperature in occurring lipases. However, lipases from extremophiles (psychrophiles, and thermophiles) are widely used to design biotransformation reactions with higher yields, fewer byproducts, or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. Lipases as a multipurpose biological catalyst have given a favorable vision in meeting the needs of several industries such as biodiesel, foods, and drinks, leather, textile, detergents, pharmaceuticals, and medicals.
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Affiliation(s)
- Gulam Rabbani
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India; Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Ejaz Ahmad
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, United States of America
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India.
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Yin Q, You S, Zhang J, Qi W, Su R. Enhancement of the polyethylene terephthalate and mono-(2-hydroxyethyl) terephthalate degradation activity of Ideonella sakaiensis PETase by an electrostatic interaction-based strategy. BIORESOURCE TECHNOLOGY 2022; 364:128026. [PMID: 36174890 DOI: 10.1016/j.biortech.2022.128026] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The serious environmental pollution that came up with the continuously growing demand for polyethylene terephthalate (PET) has attracted global concern. The IsPETase which has shown the highest PET degradation activity under ambient temperature is a promising enzyme for PET biodegradation, while poor thermostability limited its practical application. Herein, an electrostatic interaction-based strategy was applied for rational design of IsPETase towards enhanced thermostability. The IsPETaseI139R variant displayed the highest Tm value of 56.4 °C and 3.6-times higher PET degradation activity. Molecular simulations demonstrated that the introduction of salt bridges stabilized the local structures, resulting in robust thermostability. Meanwhile, the IsPETaseS92K/D157E/R251A not only exhibited higher thermostability but also showed a 1.74-fold kcat increase towards mono-(2-hydroxyethyl) terephthalate, which ultimately achieved PET depolymerization to complete monomer TPA. Collectively, the electrostatic interaction-based strategy, together with the derived IsPETase variants, could help promote the bio-recycle of PET, reducing the severe global burden of PET waste.
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Affiliation(s)
- Qingdian Yin
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Shengping You
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China
| | - Jiaxing Zhang
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Wei Qi
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China.
| | - Rongxin Su
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China
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SAPPHIRE: A stacking-based ensemble learning framework for accurate prediction of thermophilic proteins. Comput Biol Med 2022; 146:105704. [PMID: 35690478 DOI: 10.1016/j.compbiomed.2022.105704] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/15/2022] [Accepted: 06/04/2022] [Indexed: 11/22/2022]
Abstract
Thermophilic proteins (TPPs) are important in the field of protein biochemistry and development of new enzymes. Thus, computational methods must be urgently developed to accurately and rapidly identify TPPs. To date, several computational methods have been developed for TPP identification; however, few limitations in terms of performance and utility remain. In this study, we present a novel computational method, SAPPHIRE, to achieve more accurate identification of TPPs using only sequence information without any need for structural information. We combined twelve different feature encodings representing different perspectives and six popular machine learning algorithms to train 72 baseline models and extract the key information of TPPs. Subsequently, the informative predicted probabilities from the baseline models were mined and selected using a genetic algorithm in conjunction with a self-assessment-report approach. Finally, the final meta-predictor, SAPPHIRE, was built and optimized by applying an optimal feature set. The performance of SAPPHIRE in the 10-fold cross-validation test showed that a superior predictive performance compared with several baseline models could be achieved. Moreover, SAPPHIRE yielded an accuracy of 0.942 and Matthew's coefficient correlation of 0.884, which were 7.68 and 5.12% higher than those of the current existing methods, respectively, as indicated by the independent test. The proposed computational approach is anticipated to facilitate large-scale identification of TPPs and accelerate their applications in the food industry. The codes and datasets are available at https://github.com/plenoi/SAPPHIRE.
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Joshi JB, Priyadharshini R, Uthandi S. Glycosyl hydrolase 11 (xynA) gene with xylanase activity from thermophilic bacteria isolated from thermal springs. Microb Cell Fact 2022; 21:62. [PMID: 35428308 PMCID: PMC9013152 DOI: 10.1186/s12934-022-01788-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Hemicellulose is one of the copious polymer in lignocellulosic biomass (LCB). It is primarily composed of xylan linked by β-1,4 glycosidic bonds. Xylanase preferentially cleaves the β-1,4-glycosidic bonds in the xylan backbone resulting in complete hydrolysis of the biomass. Thermostable variants of glycoside hydrolases act as robust catalysts, not only in degradation but also during processing, to obtain specific carbohydrate-containing chemicals and materials (Ramasamy et al. in Madras Agric J 107(special):1. 10.29321/MAJ.2020.000382, 2020).
Results
The xylanase production by two thermophilic bacteria isolated from thermal springs was evaluated. In addition, the gene encoding this industrially vital enzyme was isolated and characterized, and its protein structure was analyzed. The thermophilic bacteria producing xylanases were isolated from augmented sawdust and banana fiber biomass from hot springs of Himachal Pradesh and identified as Bacillus subtilis VSDB5 and Bacillus licheniformis KBFB4 using 16S rRNA gene sequencing. The persistent xylanase activity revealed that the enzyme is secreted extracellularly with the maximum activity of 0.76 IU mL−1 and 1.0 IU mL−1 at 6 h and 12 h of growth by KBFB4 and VSDB5, respectively, under submerged fermentation. Both the strains exhibited the maximum activity at pH 6 and a temperature of 50 °C. The xylanases of KBFB4 and VSDB5 were thermostable and retained 40% of their activity at 60 °C after incubation for 30 min. Xylanase of VSDB5 had wide thermotolerance and retained 20% of its activity from 60 to 80 °C, whereas xylanase of KBFB4 showed wide alkali tolerance and retained 80% of its activity until pH 10. The xylanase (xynA)-encoding gene (650 bp) cloned from both the strains using specific primers showed 98 to 99% homology to β-1,4-endoxylanase gene. Further in silico analysis predicted that the xylanase protein, with a molecular weight of 23 kDa, had a high pI (9.44–9.65), which explained the alkaline nature of the enzyme and greater aliphatic index (56.29). This finding suggested that the protein is thermostable. Multiple sequence alignment and homology modeling of the protein sequence revealed that the gene product belonged to the GH11 family, indicating its possible application in bioconversion.
Conclusion
The strains B. subtilis VSDB5 and B. licheniformis KBFB4 obtained from hot springs of Himachal Pradesh produced potent and alkali-tolerant thermostable xylanases, which belong to the GH11 family. The enzyme can be supplemented in industrial applications for biomass conversion at high temperatures and pH (or in processes involving alkali treatment).
Graphical Abstract
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Ahmed Z, Zulfiqar H, Khan AA, Gul I, Dao FY, Zhang ZY, Yu XL, Tang L. iThermo: A Sequence-Based Model for Identifying Thermophilic Proteins Using a Multi-Feature Fusion Strategy. Front Microbiol 2022; 13:790063. [PMID: 35273581 PMCID: PMC8902591 DOI: 10.3389/fmicb.2022.790063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/10/2022] [Indexed: 01/20/2023] Open
Abstract
Thermophilic proteins have important application value in biotechnology and industrial processes. The correct identification of thermophilic proteins provides important information for the application of these proteins in engineering. The identification method of thermophilic proteins based on biochemistry is laborious, time-consuming, and high cost. Therefore, there is an urgent need for a fast and accurate method to identify thermophilic proteins. Considering this urgency, we constructed a reliable benchmark dataset containing 1,368 thermophilic and 1,443 non-thermophilic proteins. A multi-layer perceptron (MLP) model based on a multi-feature fusion strategy was proposed to discriminate thermophilic proteins from non-thermophilic proteins. On independent data set, the proposed model could achieve an accuracy of 96.26%, which demonstrates that the model has a good application prospect. In order to use the model conveniently, a user-friendly software package called iThermo was established and can be freely accessed at http://lin-group.cn/server/iThermo/index.html. The high accuracy of the model and the practicability of the developed software package indicate that this study can accelerate the discovery and engineering application of thermally stable proteins.
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Affiliation(s)
- Zahoor Ahmed
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hasan Zulfiqar
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Abdullah Aman Khan
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.,Sichuan Artificial Intelligence Research Institute, Yibin, China
| | - Ijaz Gul
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Tsinghua Shenzhen International Graduate School, Institute of Biopharmaceutical and Health Engineering, Tsinghua University, Shenzhen, China
| | - Fu-Ying Dao
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhao-Yue Zhang
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiao-Long Yu
- School of Materials Science and Engineering, Hainan University, Haikou, China
| | - Lixia Tang
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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15
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Gao J, Li Q, Li D. Novel Proteome and N-Glycoproteome of the Thermophilic Fungus Chaetomium thermophilum in Response to High Temperature. Front Microbiol 2021; 12:644984. [PMID: 34163440 PMCID: PMC8216556 DOI: 10.3389/fmicb.2021.644984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/22/2021] [Indexed: 11/26/2022] Open
Abstract
Thermophilic fungi are eukaryotic species that grow at high temperatures, but little is known about the underlying basis of thermophily at cell and molecular levels. Here the proteome and N-glycoproteome of Chaetomium thermophilum at varying culture temperatures (30, 50, and 55°C) were studied using hydrophilic interaction liquid chromatography enrichment and high-resolution liquid chromatography–tandem mass spectroscopy analysis. With respect to the proteome, the numbers of differentially expressed proteins were 1,274, 1,374, and 1,063 in T50/T30, T55/T30, and T55/T50, respectively. The upregulated proteins were involved in biological processes, such as protein folding and carbohydrate metabolism. Most downregulated proteins were involved in molecular functions, including structural constituents of the ribosome and other protein complexes. For the N-glycoproteome, the numbers of differentially expressed N-glycoproteins were 160, 176, and 128 in T50/T30, T55/T30, and T55/T50, respectively. The differential glycoproteins were mainly involved in various types of N-glycan biosynthesis, mRNA surveillance pathway, and protein processing in the endoplasmic reticulum. These results indicated that an efficient protein homeostasis pathway plays an essential role in the thermophily of C. thermophilum, and N-glycosylation is involved by affecting related proteins. This is the novel study to reveal thermophilic fungi’s physiological response to high-temperature adaptation using omics analysis, facilitating the exploration of the thermophily mechanism of thermophilic fungi.
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Affiliation(s)
- Jinpeng Gao
- Department of Mycology, Shandong Agricultural University, Taian, China
| | - Qingchao Li
- Department of Mycology, Shandong Agricultural University, Taian, China
| | - Duochuan Li
- Department of Mycology, Shandong Agricultural University, Taian, China
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16
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Borges B, Gallo G, Coelho C, Negri N, Maiello F, Hardy L, Würtele M. Dynamic cross correlation analysis of Thermus thermophilus alkaline phosphatase and determinants of thermostability. Biochim Biophys Acta Gen Subj 2021; 1865:129895. [PMID: 33781823 DOI: 10.1016/j.bbagen.2021.129895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/18/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Understanding the determinants of protein thermostability is very important both from the theoretical and applied perspective. One emerging view in thermostable enzymes seems to indicate that a salt bridge/charged residue network plays a fundamental role in their thermostability. METHODS The structure of alkaline phosphatase (AP) from Thermus thermophilus HB8 was solved by X-ray crystallography at 2.1 Å resolution. The obtained structure was further analyzed by molecular dynamics studies at different temperatures (303 K, 333 K and 363 K) and compared to homologous proteins from the cold-adapted organisms Shewanella sp. and Vibrio strain G15-21. To analyze differences in measures of dynamic variation, several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis were used. Using hierarchical clustering, the obtained results were combined to determine residues showing high degree dynamical variations due to temperature jumps. Furthermore, dynamic cross correlation (DCC) analysis was carried out to characterize networks of charged residues. RESULTS Top clustered residues showed a higher propensity for thermostabilizing mutations, indicating evolutionary pressure acting on thermophilic organisms. The description of rotamer distributions by Gini coefficients and Kullback-Leibler (KL) divergence both revealed significant correlations with temperature. DCC analysis revealed a significant trend to de-correlation of the movement of charged residues at higher temperatures. SIGNIFICANCE The de-correlation of charged residues detected in Thermus thermophilus AP, highlights the importance of dynamic electrostatic network interactions for the thermostability of this enzyme.
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Affiliation(s)
- Bruno Borges
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Camila Coelho
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Naiane Negri
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil; Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando Maiello
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Leon Hardy
- Department of Physics, University of South Florida, Tampa, United States
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil.
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17
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Mohsin I, Zhang LQ, Li DC, Papageorgiou AC. Crystal structure of a Cu,Zn superoxide dismutase from the thermophilic fungus Chaetomium thermophilum. Protein Pept Lett 2021; 28:1043-1053. [PMID: 33726638 DOI: 10.2174/0929866528666210316104919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Thermophilic fungi have recently emerged as a promising source of thermostable enzymes. Superoxide dismutases are key antioxidant metalloenzymes with promising therapeutic effects in various diseases, both acute and chronic. However, structural heterogeneity and low thermostability limit their therapeutic efficacy. OBJECTIVE Although several studies from hypethermophilic superoxide dismutases (SODs) have been reported, information about Cu,Zn-SODs from thermophilic fungi is scarce. Chaetomium thermophilum is a thermophilic fungus that could provide proteins with thermophilic properties. METHOD The enzyme was expressed in Pichia pastoris cells and crystallized using the vapor-diffusion method. X-ray data were collected, and the structure was determined and refined to 1.56 Å resolution. Structural analysis and comparisons were carried out. RESULTS The presence of 8 molecules (A through H) in the asymmetric unit resulted in four different interfaces. Molecules A and F form the typical homodimer which is also found in other Cu,Zn-SODs. Zinc was present in all subunits of the structure while copper was found in only four subunits with reduced occupancy (C, D, E and F). CONCLUSION The ability of the enzyme to form oligomers and the elevated Thr:Ser ratio may be contributing factors to its thermal stability. Two hydrophobic residues that participate in interface formation and are not present in other CuZn-SODs may play a role in the formation of new interfaces and the oligomerization process. The CtSOD crystal structure reported here is the first Cu,Zn-SOD structure from a thermophilic fungus.
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Affiliation(s)
- Imran Mohsin
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20521. Finland
| | - Li-Qing Zhang
- Department of Mycology, Shandong Agricultural University, Taian, Shandong 271018. China
| | - Duo-Chuan Li
- Department of Mycology, Shandong Agricultural University, Taian, Shandong 271018. China
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18
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Yang G, Mozzicafreddo M, Ballarini P, Pucciarelli S, Miceli C. An In-Silico Comparative Study of Lipases from the Antarctic Psychrophilic Ciliate Euplotes focardii and the Mesophilic Congeneric Species Euplotes crassus: Insight into Molecular Cold-Adaptation. Mar Drugs 2021; 19:md19020067. [PMID: 33513970 PMCID: PMC7912073 DOI: 10.3390/md19020067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 11/30/2022] Open
Abstract
Cold-adapted enzymes produced by psychrophilic organisms have elevated catalytic activities at low temperatures compared to their mesophilic counterparts. This is largely due to amino acids changes in the protein sequence that often confer increased molecular flexibility in the cold. Comparison of structural changes between psychrophilic and mesophilic enzymes often reveal molecular cold adaptation. In the present study, we performed an in-silico comparative analysis of 104 hydrolytic enzymes belonging to the family of lipases from two evolutionary close marine ciliate species: The Antarctic psychrophilic Euplotes focardii and the mesophilic Euplotes crassus. By applying bioinformatics approaches, we compared amino acid composition and predicted secondary and tertiary structures of these lipases to extract relevant information relative to cold adaptation. Our results not only confirm the importance of several previous recognized amino acid substitutions for cold adaptation, as the preference for small amino acid, but also identify some new factors correlated with the secondary structure possibly responsible for enhanced enzyme activity at low temperatures. This study emphasizes the subtle sequence and structural modifications that may help to transform mesophilic into psychrophilic enzymes for industrial applications by protein engineering.
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19
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Evolution of Protein Structure and Stability in Global Warming. Int J Mol Sci 2020; 21:ijms21249662. [PMID: 33352933 PMCID: PMC7767258 DOI: 10.3390/ijms21249662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each "intermediate" fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction.
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20
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Guo Z, Wang P, Liu Z, Zhao Y. Discrimination of Thermophilic Proteins and Non-thermophilic Proteins Using Feature Dimension Reduction. Front Bioeng Biotechnol 2020; 8:584807. [PMID: 33195148 PMCID: PMC7642589 DOI: 10.3389/fbioe.2020.584807] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/11/2020] [Indexed: 01/19/2023] Open
Abstract
Thermophilicity is a very important property of proteins, as it sometimes determines denaturation and cell death. Thus, methods for predicting thermophilic proteins and non-thermophilic proteins are of interest and can contribute to the design and engineering of proteins. In this article, we describe the use of feature dimension reduction technology and LIBSVM to identify thermophilic proteins. The highest accuracy obtained by cross-validation was 96.02% with 119 parameters. When using only 16 features, we obtained an accuracy of 93.33%. We discuss the importance of the different characteristics in identification and report a comparison of the performance of support vector machine to that of other methods.
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Affiliation(s)
- Zifan Guo
- School of Aeronautics and Astronautic, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Pingping Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhendong Liu
- School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China
| | - Yuming Zhao
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China
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21
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Kim IJ, Kim KH. Thermophilic l-fucose isomerase from Thermanaeromonas toyohensis for l-fucose synthesis from l-fuculose. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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Mathew GM, Madhavan A, Arun KB, Sindhu R, Binod P, Singhania RR, Sukumaran RK, Pandey A. Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications. Appl Biochem Biotechnol 2020; 193:142-164. [PMID: 32827066 DOI: 10.1007/s12010-020-03416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.
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Affiliation(s)
- Gincy M Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | | | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR - Indian Institute of Toxicology Research, Lucknow, 226 001, India.
- Frontier Research Lab, Yonsei University, Seoul, South Korea.
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23
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Miotto M, Olimpieri PP, Di Rienzo L, Ambrosetti F, Corsi P, Lepore R, Tartaglia GG, Milanetti E. Insights on protein thermal stability: a graph representation of molecular interactions. Bioinformatics 2020; 35:2569-2577. [PMID: 30535291 PMCID: PMC6662296 DOI: 10.1093/bioinformatics/bty1011] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/29/2018] [Accepted: 12/07/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Understanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing the temperature at which proteins are stable has important theoretical implications, which are intimately linked with properties of the native fold, and a wide range of potential applications from drug design to the optimization of enzyme activity. Results Here, we present a novel graph-theoretical framework to assess thermal stability based on the structure without any a priori information. In this approach we describe proteins as energy-weighted graphs and compare them using ensembles of interaction networks. Investigating the position of specific interactions within the 3D native structure, we developed a parameter-free network descriptor that permits to distinguish thermostable and mesostable proteins with an accuracy of 76% and area under the receiver operating characteristic curve of 78%. Availability and implementation Code is available upon request to edoardo.milanetti@uniroma1.it Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mattia Miotto
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, Italy.,Center for Life Nano Science@Sapienza, Instituto Italiano di Tecnologia, Viale Regina Elena, 291 Roma (RM), Italy.,Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Lorenzo Di Rienzo
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, Italy
| | - Francesco Ambrosetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, Italy.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, the Netherlands
| | - Pietro Corsi
- Department of Science, Università degli Studi "Roma Tre", via della Vasca Navale 84, Rome, Italy
| | - Rosalba Lepore
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader St. 88, Barcelona, Spain.,Institucio' Catalana de Recerca i Estudis Avancats (ICREA), 23 Passeig Lluìs Companys, Barcelona, Spain.,Department of Biology and Biotechnology, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, Italy.,Center for Life Nano Science@Sapienza, Instituto Italiano di Tecnologia, Viale Regina Elena, 291 Roma (RM), Italy
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24
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Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability. PLoS One 2020; 15:e0232959. [PMID: 32401802 PMCID: PMC7219735 DOI: 10.1371/journal.pone.0232959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for the thermostability of this enzyme. The description of rotamer distributions by Gini coefficients and Kullback–Leibler (KL) divergence both revealed significant correlations with temperature. The emerging view seems to indicate that a static salt bridge/charged residue network plays a fundamental role in the temperature resistance of Thermus thermophilus MTHFD by enhancing both electrostatic interactions and entropic energy dispersion. Furthermore, this analysis uncovered a relationship between residue mutations and evolutionary pressure acting on thermophilic organisms and thus could be of use for the design of future thermostable enzymes.
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25
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Kanagarajan S, Dhamodharan P, Mutharasappan N, Choubey SK, Jayaprakash P, Biswal J, Jeyaraman J. Structural insights on binding mechanism of CAD complexes (CPSase, ATCase and DHOase). J Biomol Struct Dyn 2020; 39:3144-3157. [PMID: 32338152 DOI: 10.1080/07391102.2020.1761877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Pyrimidine biosynthetic pathway enzymes constitute an important target for the development of antitumor drugs. To understand the role of binding mechanisms underlying the inborn errors of pyrimidine biosynthetic pathway, structure and function of enzymes have been analyzed. Pyrimidine biosynthetic pathway is initiated by CAD enzymes that harbor the first three enzymatic activities facilitated by Carbamoyl Phosphate Synthetase (CPSase), Aspartate Transcarbamoylase (ATCase) and Dihydroorotase (DHOase). While being an attractive therapeutic target, the lack of data driven us to study the CPSase (CarA and CarB) and its mode of binding to ATCase and DHOase which are the major limitation for its structural optimization. Understanding the binding mode of CPSase, ATCase and DHOase could help to identify the potential interface hotspot residues that favor the mechanism behind it. The mechanistic insight into the CAD complexes were achieved through Molecular modeling, Protein-Protein docking, Alanine scanning and Molecular dynamics (MD) Studies. The hotspot residues present in the CarB region of carboxy phosphate and carbamoyl phosphate synthetic domains are responsible for the assembly of CAD (CPSase-ATCase-DHOase) complexes. Overall analysis suggests that the identified hotspot residues were confirmed by alanine scanning and important for the regulation of pyrimidine biosynthesis. MD simulations analysis provided the prolonged stability of the interacting complexes. The present study reveals the novel hotspot residues such as Glu134, Glu147, Glu154, Asp266, Lys269, Glu274, Asp333, Trp459, Asp526, Asp528, Glu533, Glu544, Glu546, Glu800, Val855, Asp877, Tyr884 and Gln919 which could be targeted for structure-based inhibitor design to potentiate the CAD mediated regulation of aggressive tumors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Surekha Kanagarajan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Prabhu Dhamodharan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Nachiappan Mutharasappan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Sanjay Kumar Choubey
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Prajisha Jayaprakash
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jayashree Biswal
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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26
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Collier AM, Nemtsova Y, Kuber N, Banach-Petrosky W, Modak A, Sleat DE, Nanda V, Lobel P. Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1. Biochem J 2020; 477:727-745. [PMID: 31957806 PMCID: PMC8442665 DOI: 10.1042/bcj20190874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/16/2022]
Abstract
Late-infantile neuronal ceroid lipofuscinosis (LINCL) is a neurodegenerative lysosomal storage disorder caused by mutations in the gene encoding the protease tripeptidyl-peptidase 1 (TPP1). Progression of LINCL can be slowed or halted by enzyme replacement therapy, where recombinant human TPP1 is administered to patients. In this study, we utilized protein engineering techniques to increase the stability of recombinant TPP1 with the rationale that this may lengthen its lysosomal half-life, potentially increasing the potency of the therapeutic protein. Utilizing multiple structure-based methods that have been shown to increase the stability of other proteins, we have generated and evaluated over 70 TPP1 variants. The most effective mutation, R465G, increased the melting temperature of TPP1 from 55.6°C to 64.4°C and increased its enzymatic half-life at 60°C from 5.4 min to 21.9 min. However, the intracellular half-life of R465G and all other variants tested in cultured LINCL patient-derived lymphoblasts was similar to that of WT TPP1. These results provide structure/function insights into TPP1 and indicate that improving in vitro thermal stability alone is insufficient to generate TPP1 variants with improved physiological stability. This conclusion is supported by a proteome-wide analysis that indicates that lysosomal proteins have higher melting temperatures but also higher turnover rates than proteins of other organelles. These results have implications for similar efforts where protein engineering approaches, which are frequently evaluated in vitro, may be considered for improving the physiological properties of proteins, particularly those that function in the lysosomal environment.
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Affiliation(s)
- Aaron M. Collier
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Yuliya Nemtsova
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Narendra Kuber
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | | | - Anurag Modak
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
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27
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Kargar F, Mortazavi M, Torkzadeh-Mahani M, Lotfi S, Shakeri S. Evaluation of Luciferase Thermal Stability by Arginine Saturation in the Flexible Loops. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190320151005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The firefly luciferase enzyme is widely used in protein engineering and diverse
areas of biotechnology, but the main problem with this enzyme is low-temperature stability. Previous
reports indicated that surface areas of thermostable proteins are rich in arginine, which increased
their thermal stability. In this study, this aspect of thermophilic proteins evaluated by mutations of surface
residues to Arg. Here, we report the construction, purification, and studying of these mutated luciferases.
Methods:
For mutagenesis, the QuikChange site-directed mutagenesis was used and the I108R,
T156R, and N177R mutant luciferases were created. In the following, the expression and purification
of wild-type and mutant luciferases were conducted and their kinetic and structural properties were analyzed.
To analyze the role of these Arg in these loops, the 3D models of these mutants’ enzymes were
constructed in the I-TASSER server and the exact situation of these mutants was studied by the
SPDBV and PyMOL software.
Results:
Overall, the optimum temperature of these mutated enzymes was not changed. However, after
30 min incubation of these mutated enzymes at 30°C, the I108R, T156R, N177R, and wild-type kept the
80%, 50%, 20%, and 20% of their original activity, respectively. It should be noted that substitution of
these residues by Arg preserved the specific activity of firefly luciferase.
Conclusion:
Based on these results, it can be concluded that T156R and N177R mutants by compacting
local protein structure, increased the thermostability of luciferase. However, insertion of positively
charged residues in these positions create the new hydrogen bonds that associated with a series of
structural changes and confirmed by intrinsic and extrinsic fluorescence spectroscopy and homology
modeling studies.
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Affiliation(s)
- Farzane Kargar
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Shahryar Shakeri
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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28
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In silico Approach to Elucidate Factors Associated with GH1 β-Glucosidase Thermostability. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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29
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Yutani K, Matsuura Y, Joti Y. Confirmation of the formation of salt bridges in the denatured state of CutA1 protein using molecular dynamics simulations. Biophys Physicobiol 2019; 16:176-184. [PMID: 31984170 PMCID: PMC6976010 DOI: 10.2142/biophysico.16.0_176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/25/2019] [Indexed: 12/01/2022] Open
Abstract
It remains unclear how the abundant charged residues in proteins from hyperthermophiles contribute to the stabilization of proteins. Previously, based on molecular dynamics (MD) simulations, we proposed that these charged residues decrease the entropic effect by forming salt bridges in the denatured state under physiological conditions (Yutani et al., Sci. Rep. 8, 7613 (2018)). Because the quality of MD results is strongly dependent on the force fields used, in this study we performed the MD simulations using a different force field (AMBER99SB) along with the one we used before (Gromos43a1), at the same temperatures examined previously as well as at higher temperatures. In these experiments, we used the same ionic mutant (Ec0VV6) of CutA1 from Escherichia coli as in the previous study. In MD simulations at 300 K, Lys87 and Arg88 in the loop region of Ec0VV6 formed salt bridges with different favorable pairs in different force fields. Furthermore, the helical content and radius of gyration differed slightly between two force fields. However, at a higher temperature (600 K), the average numbers of salt bridges for the six substituted residues of Ec0VV6 were 0.87 per residue for Gromos43a1 and 0.88 for AMBER99SB in 400-ns MD simulation, indicating that the values were similar despite the use of different force fields. These observations suggest that the charged residues in Ec0VV6 can form a considerable number of salt bridges, even in the denatured state with drastic fluctuation at 600 K. These results corroborate our previous proposal.
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Affiliation(s)
| | | | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan.,Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198 Japan
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30
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Crystal Structure of a GH3 β-Glucosidase from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2019; 20:ijms20235962. [PMID: 31783503 PMCID: PMC6929035 DOI: 10.3390/ijms20235962] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 11/17/2022] Open
Abstract
Beta-glucosidases (β-glucosidases) have attracted considerable attention in recent years for use in various biotechnological applications. They are also essential enzymes for lignocellulose degradation in biofuel production. However, cost-effective biomass conversion requires the use of highly efficient enzymes. Thus, the search for new enzymes as better alternatives of the currently available enzyme preparations is highly important. Thermophilic fungi are nowadays considered as a promising source of enzymes with improved stability. Here, the crystal structure of a family GH3 β-glucosidase from the thermophilic fungus Chaetomium thermophilum (CtBGL) was determined at a resolution of 2.99 Å. The structure showed the three-domain architecture found in other β-glucosidases with variations in loops and linker regions. The active site catalytic residues in CtBGL were identified as Asp287 (nucleophile) and Glu517 (acid/base). Structural comparison of CtBGL with Protein Data Bank (PDB)-deposited structures revealed variations among glycosylated Asn residues. The enzyme displayed moderate glycosylation compared to other GH3 family β-glucosidases with similar structure. A new glycosylation site at position Asn504 was identified in CtBGL. Moreover, comparison with respect to several thermostability parameters suggested that glycosylation and charged residues involved in electrostatic interactions may contribute to the stability of the enzyme at elevated temperatures. The reported CtBGL structure provides additional insights into the family GH3 enzymes and could offer new ideas for further improvements in β-glucosidases for more efficient use in biotechnological applications regarding cellulose degradation.
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31
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Han M, Liao S, Peng X, Zhou X, Chen Q, Liu H. Selection and analyses of variants of a designed protein suggest importance of hydrophobicity of partially buried sidechains for protein stability at high temperatures. Protein Sci 2019; 28:1437-1447. [PMID: 31074908 DOI: 10.1002/pro.3643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 12/25/2022]
Abstract
Computationally designed proteins of high stability provide specimen in addition to natural proteins for the study of sequence-structure stability relationships at the very high end of protein stability spectrum. The melting temperature of E_1r26, a protein we previously designed using the A Backbone-based Amino aCid Usage Survey (ABACUS) sequence design program, is above 110 °C, more than 50 °C higher than that of the natural thioredoxin protein whose backbone (PDB ID 1R26) has been used as the design target. Using an experimental selection approach, we obtained variants of E_1r26 that remain folded but are of reduced stability, including one whose unfolding temperature and denaturing guanidine concentration are similar to those of 1r26. The mutant unfolds with a certain degree of cooperativity. Its structure solved by X-ray crystallography agrees with that of 1r26 by a root mean square deviation of 1.3 Å, adding supports to the accuracy of the ABACUS method. Analyses of intermediate mutants indicate that the substitution of two partially buried hydrophobic residues (isoleucine and leucine) by polar residues (threonine and serine, respectively) are responsible for the dramatic change in the unfolding temperature. It is suggested that the effects of mutations located in rigid secondary structure regions, but not those in loops, may be well predicted through ABACUS mutation energy analysis. The results also suggest that hydrophobic effects involving intermediately buried sidechains can be critically important for protein stability at high temperatures.
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Affiliation(s)
- Mingjie Han
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Sanhui Liao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiong Peng
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaoqun Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Quan Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.,School of Data Science, University of Science and Technology of China, Hefei, Anhui, China.,Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, China
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32
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Lu M, Dukunde A, Daniel R. Biochemical profiles of two thermostable and organic solvent-tolerant esterases derived from a compost metagenome. Appl Microbiol Biotechnol 2019; 103:3421-3437. [PMID: 30809711 DOI: 10.1007/s00253-019-09695-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022]
Abstract
Owing to the functional versatility and potential applications in industry, interest in lipolytic enzymes tolerant to organic solvents is increasing. In this study, functional screening of a compost soil metagenome resulted in identification of two lipolytic genes, est1 and est2, encoding 270 and 389 amino acids, respectively. The two genes were heterologously expressed and characterized. Est1 and Est2 are thermostable enzymes with optimal enzyme activities at 80 and 70 °C, respectively. A second-order rotatable design, which allows establishing the relationship between multiple variables with the obtained responses, was used to explore the combined effects of temperature and pH on esterase stability. The response curve indicated that Est1, and particularly Est2, retained high stability within a broad range of temperature and pH values. Furthermore, the effects of organic solvents on Est1 and Est2 activities and stabilities were assessed. Notably, Est2 activity was significantly enhanced (two- to tenfold) in the presence of ethanol, methanol, isopropanol, and 1-propanol over a concentration range between 6 and 30% (v/v). For the short-term stability (2 h of incubation), Est2 exhibited high tolerance against 60% (v/v) of ethanol, methanol, isopropanol, DMSO, and acetone, while Est1 activity resisted these solvents only at lower concentrations (below 30%, v/v). Est2 also displayed high stability towards some water-immiscible organic solvents, such as ethyl acetate, diethyl ether, and toluene. With respect to long-term stability, Est2 retained most of its activity after 26 days of incubation in the presence of 30% (v/v) ethanol, methanol, isopropanol, DMSO, or acetone. All of these features indicate that Est1 and Est2 possess application potential.
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Affiliation(s)
- Mingji Lu
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Amélie Dukunde
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany.
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33
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Hu G, Wang K, Song J, Uversky VN, Kurgan L. Taxonomic Landscape of the Dark Proteomes: Whole-Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity. Proteomics 2018; 18:e1800243. [PMID: 30198635 DOI: 10.1002/pmic.201800243] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/30/2018] [Indexed: 12/14/2022]
Abstract
Growth rate of the protein sequence universe dramatically exceeds the speed of expansion for the protein structure universe, generating an immense dark proteome that includes proteins with unknown structure. A whole-proteome scale analysis of 5.4 million proteins from 987 proteomes in the three domains of life and viruses to systematically dissect an interplay between structural coverage, degree of putative intrinsic disorder, and predicted propensity for structure determination is performed. It has been found that Archaean and Bacterial proteomes have relatively high structural coverage and low amounts of disorder, whereas Eukaryotic and Viral proteomes are characterized by a broad spread of structural coverage and higher disorder levels. The analysis reveals that dark proteomes (i.e., proteomes containing high fractions of proteins with unknown structure) have significantly elevated amounts of intrinsic disorder and are predicted to be difficult to solve structurally. Although the majority of dark proteomes are of viral origin, many dark viral proteomes have at least modest crystallization propensity and only a handful of them are enriched in the intrinsic disorder. The disorder, structural coverage, and propensity are mapped for structural determination onto a novel proteome-level sequence similarity network to analyze the interplay of these characteristics in the taxonomic landscape.
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Affiliation(s)
- Gang Hu
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, P. R. China
| | - Kui Wang
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, P. R. China
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, 33612, USA.,Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
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34
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Chakravorty D, Patra S. RankProt: A multi criteria-ranking platform to attain protein thermostabilizing mutations and its in vitro applications - Attribute based prediction method on the principles of Analytical Hierarchical Process. PLoS One 2018; 13:e0203036. [PMID: 30286107 PMCID: PMC6171822 DOI: 10.1371/journal.pone.0203036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/14/2018] [Indexed: 01/15/2023] Open
Abstract
Attaining recombinant thermostable proteins is still a challenge for protein engineering. The complexity is the length of time and enormous efforts required to achieve the desired results. Present work proposes a novel and economic strategy of attaining protein thermostability by predicting site-specific mutations at the shortest possible time. The success of the approach can be attributed to Analytical Hierarchical Process and the outcome was a rationalized thermostable mutation(s) prediction tool- RankProt. Briefly the method involved ranking of 17 biophysical protein features as class predictors, derived from 127 pairs of thermostable and mesostable proteins. Among the 17 predictors, ionic interactions and main-chain to main-chain hydrogen bonds were the highest ranked features with eigen value of 0.091. The success of the tool was judged by multi-fold in silico validation tests and it achieved the prediction accuracy of 91% with AUC 0.927. Further, in vitro validation was carried out by predicting thermostabilizing mutations for mesostable Bacillus subtilis lipase and performing the predicted mutations by multi-site directed mutagenesis. The rationalized method was successful to render the lipase thermostable with optimum temperature stability and Tm increase by 20°C and 7°C respectively. Conclusively it can be said that it was the minimum number of mutations in comparison to the number of mutations incorporated to render Bacillus subtilis lipase thermostable, by directed evolution techniques. The present work shows that protein stabilizing mutations can be rationally designed by balancing the biophysical pleiotropy of proteins, in accordance to the selection pressure.
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Affiliation(s)
- Debamitra Chakravorty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- * E-mail:
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35
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Ion-ion interactions in the denatured state contribute to the stabilization of CutA1 proteins. Sci Rep 2018; 8:7613. [PMID: 29769700 PMCID: PMC5955972 DOI: 10.1038/s41598-018-25825-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/30/2018] [Indexed: 12/11/2022] Open
Abstract
In order to elucidate features of the denatured state ensembles that exist in equilibrium with the native state under physiological conditions, we performed 1.4-μs molecular dynamics (MD) simulations at 400 K and 450 K using the monomer subunits of three CutA1 mutants from Escherichia coli: an SH-free mutant (Ec0SH) with denaturation temperature (Td) = 85.6 °C, a hydrophobic mutant (Ec0VV) with Td = 113.3 °C, and an ionic mutant (Ec0VV_6) with Td = 136.8 °C. The occupancy of salt bridges by the six substituted charged residues in Ec0VV_6 was 140.1% at 300 K and 89.5% at 450 K, indicating that even in the denatured state, salt bridge occupancy was high, approximately 60% of that at 300 K. From these results, we can infer that proteins from hyperthermophiles with a high ratio of charged residues are stabilized by a decrease in conformational entropy due to ion–ion interactions in the denatured state. The mechanism must be comparable to the stabilization conferred by disulfide bonds within a protein. This suggests that introduction of charged residues, to promote formation of salt bridges in the denatured state, would be a simple way to rationally design stability-enhanced mutants.
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36
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Matsuura Y, Takehira M, Makhatadze GI, Joti Y, Naitow H, Kunishima N, Yutani K. Strategy for Stabilization of CutA1 Proteins Due to Ion-Ion Interactions at Temperatures of over 100 °C. Biochemistry 2018; 57:2649-2656. [PMID: 29648806 DOI: 10.1021/acs.biochem.8b00103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In order to elucidate the contribution of charged residues to protein stabilization at temperatures of over 100 °C, we constructed many mutants of the CutA1 protein ( EcCutA1) from Escherichia coli. The goal was to see if one can achieve the same stability as for a CutA1 from hyperthermophile Pyrococcus horikoshii that has the denaturation temperature near 150 °C. The hydrophobic mutant of EcCutA1 ( Ec0VV) with denaturation temperature ( Td) of 113.2 °C was used as a template for mutations. The highest Td of Ec0VV mutants substituted by a single charged residue was 118.4 °C. Multiple ion mutants were also constructed by combination of single mutants and found to have an increased thermostability. The highest stability of multiple mutants was a mutant substituted by nine charged residues that had a Td of 142.2 °C. To evaluate the energy of ion-ion interactions of mutant proteins, we used the structural ensemble obtained by a molecular dynamics simulation at 300 K. The Td of ionic mutants linearly increases with the increments of the computed energy of ion-ion interactions for ionic mutant proteins even up to the temperatures near 140 °C, suggesting that ion-ion interactions cumulatively contribute to the stabilization of a protein at high temperatures.
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Affiliation(s)
| | - Michiyo Takehira
- RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan
| | - George I Makhatadze
- Department of Biology , Rensselaer Polytechnic Institute , 110 Eighth Street , Troy , New York 12180-3590 , United States
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute , 1-1-1, Kouto , Sayo, Hyogo 679-5198 Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan
| | - Naoki Kunishima
- RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan
| | - Katsuhide Yutani
- RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan
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37
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Okafor CD, Pathak MC, Fagan CE, Bauer NC, Cole MF, Gaucher EA, Ortlund EA. Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus. Structure 2018; 26:118-129.e3. [PMID: 29276038 PMCID: PMC5785943 DOI: 10.1016/j.str.2017.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/18/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023]
Abstract
Rationally engineering thermostability in proteins would create enzymes and receptors that function under harsh industrial applications. Several sequence-based approaches can generate thermostable variants of mesophilic proteins. To gain insight into the mechanisms by which proteins become more stable, we use structural and dynamic analyses to compare two popular approaches, ancestral sequence reconstruction (ASR) and the consensus method, used to generate thermostable variants of Elongation Factor Thermo-unstable (EF-Tu). We present crystal structures of ancestral and consensus EF-Tus, accompanied by molecular dynamics simulations aimed at probing the strategies employed to enhance thermostability. All proteins adopt crystal structures similar to extant EF-Tus, revealing no difference in average structure between the methods. Molecular dynamics reveals that ASR-generated sequences retain dynamic properties similar to extant, thermostable EF-Tu from Thermus aquaticus, while consensus EF-Tu dynamics differ from evolution-based sequences. This work highlights the advantage of ASR for engineering thermostability while preserving natural motions in multidomain proteins.
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Affiliation(s)
- C. Denise Okafor
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA
| | - Manish C. Pathak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA
| | - Crystal E. Fagan
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA
| | - Nicholas C. Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA
| | - Megan F. Cole
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332 USA
| | - Eric A. Gaucher
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332 USA
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 USA,Correspondence:
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38
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Amadei A, Del Galdo S, D'Abramo M. Density discriminates between thermophilic and mesophilic proteins. J Biomol Struct Dyn 2017; 36:3265-3273. [PMID: 28952426 DOI: 10.1080/07391102.2017.1385537] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Despite an intense interest and a remarkable number of studies on the subject, the relationships between thermostability and (primary, secondary and tertiary) structure of proteins are still not fully understood. Here, comparing the protein density - defined by the ratio between the residue number and protein excluded volume - for a set of thermophilic/mesophilic pairs, we provide evidence that this property is connected to the optimal growth temperature. In particular, our results indicate that thermophilic proteins have - in general - a lower density with respect to the mesophilic counterparts, being such a correlation more pronounced for optimal growth temperature differences greater than 40°C. The effect of the protein thermostability changes on the molecular shape is also presented.
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Affiliation(s)
- Andrea Amadei
- a Department of Chemical Science and Technology , University of Roma Tor Vergata , via della Ricerca Scientifica, 00133 , Roma , Italy
| | - Sara Del Galdo
- a Department of Chemical Science and Technology , University of Roma Tor Vergata , via della Ricerca Scientifica, 00133 , Roma , Italy
| | - Marco D'Abramo
- b Department of Chemistry , Sapienza University of Rome , P.le A. Moro, 5, 00185 , Rome , Italy
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39
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Singh MK, Shivakumaraswamy S, Gummadi SN, Manoj N. Role of an N-terminal extension in stability and catalytic activity of a hyperthermostable α/β hydrolase fold esterase. Protein Eng Des Sel 2017; 30:559-570. [PMID: 28967962 DOI: 10.1093/protein/gzx049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022] Open
Abstract
The carbohydrate esterase family 7 (CE7) enzymes catalyze the deacetylation of acetyl esters of a broad range of alcohols and is unique in its activity towards cephalosporin C. The CE7 fold contains a conserved N-terminal extension that distinguishes it from the canonical α/β hydrolase fold. The hexameric quaternary structure indicates that the N-terminus may affect activity and specificity by controlling access of substrates to the buried active sites via an entrance tunnel. In this context, we characterized the catalytic parameters, conformation and thermal stability of two truncation variants lacking four and ten residues of the N-terminal region of the hyperthermostable Thermotoga maritima CE7 acetyl esterase (TmAcE). The truncations did not affect the secondary structure or the fold but modulated the oligomerization dynamics. A modest increase was observed in substrate specificity for acetylated xylose compared with acetylated glucose. A drastic reduction of ~30-40°C in the optimum temperature for activity of the variants indicated lower thermal stability. The loss of hyperthermostability appears to be an indirect effect associated with an increase in the conformational flexibility of an otherwise rigid neighboring loop containing a catalytic triad residue. The results suggest that the N-terminal extension was evolutionarily selected to preserve the stability of the enzyme.
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Affiliation(s)
- Mrityunjay K Singh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Santosh Shivakumaraswamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Sathyanarayana N Gummadi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
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40
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Volk K, Breunig SD, Rid R, Herzog J, Bräuer M, Hundsberger H, Klein C, Müller N, Önder K. Structural analysis and interaction studies of acyl-carrier protein (acpP) of Staphylococcus aureus, an extraordinarily thermally stable protein. Biol Chem 2017; 398:125-133. [PMID: 27467752 DOI: 10.1515/hsz-2016-0185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/22/2016] [Indexed: 11/15/2022]
Abstract
Acyl-carrier-protein (acpP) is an essential protein in fatty acid biosynthesis of Staphylococcus aureus [Cronan, J.E. and Thomas, J. (2009). Complex enzymes in microbial natural product biosynthesis, part B: polyketides, aminocoumarins and carbohydrates. METHOD Enzymol. 459, 395-433; Halavaty, A.S., Kim, Y., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Zhou, M., Onopriyenko, O., Skarina, T., Papazisi, L., et al. (2012). Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria. Acta Crystallogr. Sect. D Biol. Crystallogr. 68, 1359-1370]. The inactive apo-form is converted to the active holo-enzyme by acyl-carrier protein synthase (acpS) through addition of a 4'-phosphopantetheine group from coenzyme A to a conserved serine residue of acpP [Flugel, R.S., Hwangbo, Y., Lambalot, R.H., Cronan, J.E., and Walsh, C.T. (2000). Holo-(acyl-carrier protein) synthase and phosphopantetheinyl transfer in Escherichia coli. J. Biol. Chem. 275, 959-968; Lambalot, R.H. and Walsh, C.T. (1995). Cloning, overproduction, and characterization of the Escherichia coli holo-acyl-carrier protein synthase. J. Biol. Chem. 270, 24658-24661]. Once activated, acpP acts as an anchor for the growing fatty acid chain. Structural data from X-ray crystallographic analysis reveals that, despite its small size (8 kDa), acpP adopts a distinct, mostly α-helical structure when complexed with acpS [Halavaty, A.S., Kim, Y., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Zhou, M., Onopriyenko, O., Skarina, T., Papazisi, L., et al. (2012). Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria. Acta Crystallogr. Sect. D Biol. Crystallogr. 68, 1359-1370; Byers, D.M. and Gong, H. (2007). Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family. Biochem. Cell Biol. 85, 649-662]. We expressed and purified recombinant, active S. aureus acpP from Escherichia coli and mimicked the beginning of fatty acid biosynthesis by employing an [14C]-acp loading assay. Surprisingly, acpP remained functional even after heat treatment at 95°C for up to 10 min. NMR data from 2D-HSQC experiments as well as interaction studies with acpS confirmed that acpP is structured and active both before and after heat treatment, with no significant differences between the two. Thus, our data suggest that S. aureus acpP is a highly stable protein capable of maintaining its structure at high temperatures.
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41
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Khan M, Sathya TA. Extremozymes from metagenome: Potential applications in food processing. Crit Rev Food Sci Nutr 2017; 58:2017-2025. [PMID: 28605203 DOI: 10.1080/10408398.2017.1296408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The long-established use of enzymes for food processing and product formulation has resulted in an increased enzyme market compounding to 7.0% annual growth rate. Advancements in molecular biology and recognition that enzymes with specific properties have application for industrial production of infant, baby and functional foods boosted research toward sourcing the genes of microorganisms for enzymes with distinctive properties. In this regard, functional metagenomics for extremozymes has gained attention on the premise that such enzymes can catalyze specific reactions. Hence, metagenomics that can isolate functional genes of unculturable extremophilic microorganisms has expanded attention as a promising tool. Developments in this field of research in relation to food sector are reviewed.
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Affiliation(s)
- Mahejibin Khan
- a CSIR-Central Food Technological Research Institute-Resource Centre Lucknow , India.,c Academy of Scientific and Innovative Research , New Delhi , India
| | - T A Sathya
- b CSIR-Central Food Technological Research Institute , Mysore , India.,c Academy of Scientific and Innovative Research , New Delhi , India
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Goins CM, Dajnowicz S, Thanna S, Sucheck SJ, Parks JM, Ronning DR. Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives. ACS Infect Dis 2017; 3:378-387. [PMID: 28285521 DOI: 10.1021/acsinfecdis.7b00003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Previous studies identified ebselen as a potent in vitro and in vivo inhibitor of the Mycobacterium tuberculosis (Mtb) antigen 85 (Ag85) complex, comprising three homologous enzymes required for the biosynthesis of the mycobacterial cell wall. In this study, the Mtb Ag85C enzyme was cocrystallized with azido and adamantyl ebselen derivatives, resulting in two crystallographic structures of 2.01 and 1.30 Å resolution, respectively. Both structures displayed the anticipated covalent modification of the solvent accessible, noncatalytic Cys209 residue forming a selenenylsulfide bond. Continuous difference density for both thiol modifiers allowed for the assessment of interactions that influence ebselen binding and inhibitor orientation that were unobserved in previous Ag85C ebselen structures. The kinact/KI values for ebselen, adamantyl ebselen, and azido ebselen support the importance of observed constructive chemical interactions with Arg239 for increased in vitro efficacy toward Ag85C. To better understand the in vitro kinetic properties of these ebselen derivatives, the energetics of specific protein-inhibitor interactions and relative reaction free energies were calculated for ebselen and both derivatives using density functional theory. These studies further support the different in vitro properties of ebselen and two select ebselen derivatives from our previously published ebselen library with respect to kinetics and protein-inhibitor interactions. In both structures, the α9 helix was displaced farther from the enzyme active site than the previous Ag85C ebselen structure, resulting in the restructuring of a connecting loop and imparting a conformational change to residues believed to play a role in substrate binding specific to Ag85C. These notable structural changes directly affect protein stability, reducing the overall melting temperature by up to 14.5 °C, resulting in the unfolding of protein at physiological temperatures. Additionally, this structural rearrangement due to covalent allosteric modification creates a sizable solvent network that encompasses the active site and extends to the modified Cys209 residue. In all, this study outlines factors that influence enzyme inhibition by ebselen and its derivatives while further highlighting the effects of the covalent modification of Cys209 by said inhibitors on the structure and stability of Ag85C. Furthermore, the results suggest a strategy for developing new classes of Ag85 inhibitors with increased specificity and potency.
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Affiliation(s)
- Christopher M. Goins
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Steven Dajnowicz
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sandeep Thanna
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Steven J. Sucheck
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics,
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Donald R. Ronning
- Department of Chemistry
and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
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43
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Identification of potential inhibitors for oncogenic target of dihydroorotate dehydrogenase using in silico approaches. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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de Souza AR, de Araújo GC, Zanphorlin LM, Ruller R, Franco FC, Torres FA, Mertens JA, Bowman MJ, Gomes E, Da Silva R. Engineering increased thermostability in the GH-10 endo-1,4-β-xylanase from Thermoascus aurantiacus CBMAI 756. Int J Biol Macromol 2016; 93:20-26. [DOI: 10.1016/j.ijbiomac.2016.08.056] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/13/2016] [Accepted: 08/20/2016] [Indexed: 12/13/2022]
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45
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Gindt YM, Edani BH, Olejnikova A, Roberts AN, Munshi S, Stanley RJ. The Missing Electrostatic Interactions Between DNA Substrate and Sulfolobus solfataricus DNA Photolyase: What is the Role of Charged Amino Acids in Thermophilic DNA Binding Proteins? J Phys Chem B 2016; 120:10234-10242. [PMID: 27626127 DOI: 10.1021/acs.jpcb.6b07201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA photolyase can be used to study how a protein with its required cofactor has adapted over a large temperature range. The enzymatic activity and thermodynamics of substrate binding for protein from Sulfolobus solfataricus were directly compared to protein from Escherichia coli. Turnover numbers and catalytic activity were virtually identical, but organic cosolvents may be necessary to maintain activity of the thermophilic protein at higher temperatures. UV-damaged DNA binding to the thermophilic protein is less favorable by ∼2 kJ/mol. The enthalpy of binding is ∼10 kJ/mol less exothermic for the thermophile, but the amount and type of surface area buried upon DNA binding appears to be somewhat similar. The most important finding was observed when ionic strength studies were used to separate binding interactions into electrostatic and nonelectrostatic contributions; DNA binding to the thermophilic protein appears to lack the electrostatic contributions observed with the mesophilic protein.
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Affiliation(s)
- Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Ban H Edani
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Antonia Olejnikova
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Ariana N Roberts
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Sudipto Munshi
- Department of Chemistry, Temple University , 1801 N Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University , 1801 N Broad Street, Philadelphia, Pennsylvania 19122, United States
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46
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Du X, Sang P, Xia YL, Li Y, Liang J, Ai SM, Ji XL, Fu YX, Liu SQ. Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:1500-1517. [PMID: 27485684 DOI: 10.1080/07391102.2016.1188155] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, and 573 K). The comparative analyses of MD trajectories reveal that at almost all temperatures, VPR exhibits greater structural fluctuations/deviations, more unstable regular secondary structural elements, and higher global flexibility than PRK. Although these two proteases follow similar unfolding pathways at high temperatures, VPR initiates unfolding at a lower temperature and unfolds faster at the same high temperatures than PRK. These observations collectively indicate that VPR is less stable and more heat-labile than PRK. Analyses of the structural/geometrical properties reveal that, when compared to PRK, VPR has larger radius of gyration (Rg), less intramolecular contacts and hydrogen bonds (HBs), more protein-solvent HBs, and smaller burial of nonpolar area and larger exposure of polar area. These suggest that the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area, whereas the enhanced stability of PRK could be ascribed to its increased intramolecular interactions arising from the better optimized hydrophobicity. The factors responsible for the significant differences in local flexibility between these two proteases were also analyzed and ascertained. This study provides insights into molecular basis of thermostability of homologous serine proteases adapted to different temperatures.
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Affiliation(s)
- Xing Du
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Peng Sang
- b Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming 650032 , PR China
| | - Yuan-Ling Xia
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Yi Li
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Jing Liang
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Shi-Meng Ai
- c Department of Applied Mathematics , Yunnan Agricultural University , Kunming 650201 , PR China
| | - Xing-Lai Ji
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,d Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences , Yunnan University , Kunming 650223 , PR China
| | - Yun-Xin Fu
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,e Human Genetics Center and Division of Biostatistics, School of Public Health , The University of Texas Health Science Center , Houston , TX , 77030 , USA
| | - Shu-Qun Liu
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,d Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences , Yunnan University , Kunming 650223 , PR China
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Kakagianni M, Gougouli M, Koutsoumanis KP. Development and application of Geobacillus stearothermophilus growth model for predicting spoilage of evaporated milk. Food Microbiol 2016; 57:28-35. [DOI: 10.1016/j.fm.2016.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 12/07/2015] [Accepted: 01/09/2016] [Indexed: 10/22/2022]
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48
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Tych KM, Batchelor M, Hoffmann T, Wilson MC, Hughes ML, Paci E, Brockwell DJ, Dougan L. Differential Effects of Hydrophobic Core Packing Residues for Thermodynamic and Mechanical Stability of a Hyperthermophilic Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7392-7402. [PMID: 27338140 DOI: 10.1021/acs.langmuir.6b01550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins from organisms that have adapted to environmental extremes provide attractive systems to explore and determine the origins of protein stability. Improved hydrophobic core packing and decreased loop-length flexibility can increase the thermodynamic stability of proteins from hyperthermophilic organisms. However, their impact on protein mechanical stability is not known. Here, we use protein engineering, biophysical characterization, single-molecule force spectroscopy (SMFS), and molecular dynamics (MD) simulations to measure the effect of altering hydrophobic core packing on the stability of the cold shock protein TmCSP from the hyperthermophilic bacterium Thermotoga maritima. We make two variants of TmCSP in which a mutation is made to reduce the size of aliphatic groups from buried hydrophobic side chains. In the first, a mutation is introduced in a long loop (TmCSP L40A); in the other, the mutation is introduced on the C-terminal β-strand (TmCSP V62A). We use MD simulations to confirm that the mutant TmCSP L40A shows the most significant increase in loop flexibility, and mutant TmCSP V62A shows greater disruption to the core packing. We measure the thermodynamic stability (ΔGD-N) of the mutated proteins and show that there is a more significant reduction for TmCSP L40A (ΔΔG = 63%) than TmCSP V62A (ΔΔG = 47%), as might be expected on the basis of the relative reduction in the size of the side chain. By contrast, SMFS measures the mechanical stability (ΔG*) and shows a greater reduction for TmCSP V62A (ΔΔG* = 8.4%) than TmCSP L40A (ΔΔG* = 2.5%). While the impact on the mechanical stability is subtle, the results demonstrate the power of tuning noncovalent interactions to modulate both the thermodynamic and mechanical stability of a protein. Such understanding and control provide the opportunity to design proteins with optimized thermodynamic and mechanical properties.
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Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Matthew Batchelor
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Michael C Wilson
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Megan L Hughes
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Emanuele Paci
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
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49
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Su JG, Han XM, Zhao SX, Hou YX, Li XY, Qi LS, Wang JH. Impacts of the charged residues mutation S48E/N62H on the thermostability and unfolding behavior of cold shock protein: insights from molecular dynamics simulation with Gō model. J Mol Model 2016; 22:91. [DOI: 10.1007/s00894-016-2958-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/07/2016] [Indexed: 10/22/2022]
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50
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Chen L, Li X, Wang R, Fang F, Yang W, Kan W. Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation. J Biomol Struct Dyn 2016; 34:1576-89. [DOI: 10.1080/07391102.2015.1084480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Xue Li
- College of Chemistry and Biology, Beihua Uuniversity, Jilin 132000, P.R. China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Fengqin Fang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Wanli Yang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Wei Kan
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
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