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Sundar Panja A. The systematic codon usage bias has an important effect on genetic adaption in native species. Gene 2024; 926:148627. [PMID: 38823656 DOI: 10.1016/j.gene.2024.148627] [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: 02/06/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.
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Affiliation(s)
- Anindya Sundar Panja
- Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal 721102, India.
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2
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Hong SY, Yoon J, An YJ, Lee S, Cha HG, Pandey A, Yoo YJ, Joo JC. Statistical Analysis of the Role of Cavity Flexibility in Thermostability of Proteins. Polymers (Basel) 2024; 16:291. [PMID: 38276699 PMCID: PMC10819066 DOI: 10.3390/polym16020291] [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: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Conventional statistical investigations have primarily focused on the comparison of the simple one-dimensional characteristics of protein cavities, such as number, surface area, and volume. These studies have failed to discern the crucial distinctions in cavity properties between thermophilic and mesophilic proteins that contribute to protein thermostability. In this study, the significance of cavity properties, i.e., flexibility and location, in protein thermostability was investigated by comparing structural differences between homologous thermophilic and mesophilic proteins. Three dimensions of protein structure were categorized into three regions (core, boundary, and surface) and a comparative analysis of cavity properties using this structural index was conducted. The statistical analysis revealed that cavity flexibility is closely related to protein thermostability. The core cavities of thermophilic proteins were less flexible than those of mesophilic proteins (averaged B' factor values, -0.6484 and -0.5111), which might be less deleterious to protein thermostability. Thermophilic proteins exhibited fewer cavities in the boundary and surface regions. Notably, cavities in mesophilic proteins, across all regions, exhibited greater flexibility than those in thermophilic proteins (>95% probability). The increased flexibility of cavities in the boundary and surface regions of mesophilic proteins, as opposed to thermophilic proteins, may compromise stability. Recent protein engineering investigations involving mesophilic xylanase and protease showed results consistent with the findings of this study, suggesting that the manipulation of flexible cavities in the surface region can enhance thermostability. Consequently, our findings suggest that a rational or computational approach to the design of flexible cavities in surface or boundary regions could serve as an effective strategy to enhance the thermostability of mesophilic proteins.
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Affiliation(s)
- So Yeon Hong
- Department of Chemical and Biological Engineering, Inha Technical College, Inha-ro 100, Michuhol-gu, Incheon 22212, Republic of Korea;
| | - Jihyun Yoon
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
| | - Young Joo An
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
| | - Siseon Lee
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
| | - Haeng-Geun Cha
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
| | - Ashutosh Pandey
- Institute for Water and Wastewater Technology, Durban University of Technology, 19 Steve Biko Road, Durban 4000, South Africa;
- Department of Biotechnology, Faculty of Life Science and Technology, AKS University, Satna 485001, Madhya Pradesh, India
| | - Young Je Yoo
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea;
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si 14662, Republic of Korea (S.L.)
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3
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Shen L, Liu Y, Chen L, Lei T, Ren P, Ji M, Song W, Lin H, Su W, Wang S, Rooman M, Pucci F. Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group. THE ISME JOURNAL 2024; 18:wrad020. [PMID: 38365240 PMCID: PMC10837837 DOI: 10.1093/ismejo/wrad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.
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Affiliation(s)
- Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu 241000, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tingting Lei
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wei Su
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
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Senthilkumar S, Mahesh S, Jaisankar S, Yennamalli RM. Surface exposed and charged residues drive thermostability in fungi. Proteins 2023. [PMID: 37909647 DOI: 10.1002/prot.26623] [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: 05/18/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023]
Abstract
Fungi, though mesophilic, include thermophilic and thermostable species, as well. The thermostability of proteins observed in these fungi is most likely to be attributed to several molecular factors, such as the presence of salt bridges and hydrogen bond interactions between side chains. These factors cannot be generalized for all fungi. Factors impacting thermostability can guide how fungal thermophilic proteins gain thermostability. We curated a dataset of proteins for 14 thermophilic fungi and their evolutionarily closer mesophiles. Additionally, the proteome of Chaetomium thermophilum and its evolutionarily related mesophile Chaetomium globosum was analyzed. Using eggNOG, we categorized the proteomes into clusters of orthologous groups (COGs). While the individual count of proteins is over-represented in mesophiles (for COGs S, G, L, and Q), there are certain features that are significantly enriched in thermophiles (such as charged residues, exposed residues, polar residues, etc.). Since fungi are known to be cellulolytic and chitinolytic by nature, we selected 37 existing carbohydrate-active enzymes (CAZyme) families in Eurotiales, Mucorales, and Sordariales. We looked at closely similar sequences and their modeled structures for further comparison. Comparing solvent accessibilities of thermophilic and mesophilic proteins, exposed and intermediate residues are observed higher in thermophiles whereas buried residues are observed higher in mesophiles. For specific five CAZYme families (GH7, GH11, GH18, GH45, and CBM1) we looked at position-specific substitutions between thermophiles and mesophiles. We also found that there are relatively more intramolecular interactions in thermophiles compared to mesophiles. Thus, we found factors such as surface exposed residues and charged residues that are highly likely to impart thermostability in fungi, and this study sets the stage for further studies in the area of fungal thermostability.
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Affiliation(s)
- Shricharan Senthilkumar
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Sankar Mahesh
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Subachandran Jaisankar
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Lamolle G, Simón D, Iriarte A, Musto H. Main Factors Shaping Amino Acid Usage Across Evolution. J Mol Evol 2023:10.1007/s00239-023-10120-5. [PMID: 37264211 DOI: 10.1007/s00239-023-10120-5] [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: 03/22/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
The standard genetic code determines that in most species, including viruses, there are 20 amino acids that are coded by 61 codons, while the other three codons are stop triplets. Considering the whole proteome each species features its own amino acid frequencies, given the slow rate of change, closely related species display similar GC content and amino acids usage. In contrast, distantly related species display different amino acid frequencies. Furthermore, within certain multicellular species, as mammals, intragenomic differences in the usage of amino acids are evident. In this communication, we shall summarize some of the most prominent and well-established factors that determine the differences found in the amino acid usage, both across evolution and intragenomically.
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Affiliation(s)
- Guillermo Lamolle
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
| | - Diego Simón
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay.
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Li ZL, Buck M. A proteome-scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics. Proteins 2023; 91:3-15. [PMID: 36053994 PMCID: PMC10087973 DOI: 10.1002/prot.26404] [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: 01/23/2022] [Revised: 07/06/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
Despite differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins, often with subtle differences in amino acid sequence. Here, we present a simple way to analyze the difference in amino acid occurrence by comparing highly homologous proteins on a subproteome level between several vertebrate model organisms. Specifically, we use this method to identify a pattern of amino acid conservation as well as a shift in amino acid occurrence between homeotherms (warm-blooded species) and poikilotherms (cold-blooded species). Importantly, this general analysis and a specific example further establish a broad correlation, if not likely connection between the thermal adaptation of protein sequences and two of their physical features: on average a change in their protein dynamics and, even more strongly, in their solvation. For poikilotherms, such as frog and fish, the lower body temperature is expected to increase the protein-protein interaction due to a decrease in protein internal dynamics. In order to counteract the tendency for enhanced binding caused by low temperatures, poikilotherms enhance the solvation of their proteins by favoring polar amino acids. This feature appears to dominate over possible changes in dynamics for some proteins. The results suggest that a general trend for amino acid choice is part of the mechanism for thermoadaptation of vertebrate organisms at the molecular level.
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Affiliation(s)
- Zhen-Lu Li
- School of Life Science, Tianjin University, Tianjin, China.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Departments of Pharmacology and of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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7
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Nguyen C, Yearwood LM, McCully ME. Thermostabilization mechanisms in thermophilic versus mesophilic three-helix bundle proteins. J Comput Chem 2022; 43:197-205. [PMID: 34738662 PMCID: PMC8665064 DOI: 10.1002/jcc.26782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/22/2021] [Accepted: 10/24/2021] [Indexed: 11/21/2022]
Abstract
The engineered three‐helix bundle, UVF, is thermostabilized entropically due to heightened, native‐state dynamics. However, it is unclear whether this thermostabilization strategy is observed in natural proteins from thermophiles. We performed all‐atom, explicit solvent molecular dynamics simulations of two three‐helix bundles from thermophilic H. butylicus (2lvsN and 2lvsC) and compared their dynamics to a mesophilic three‐helix bundle, the Engrailed homeodomain (EnHD). Like UVF, 2lvsC had heightened native dynamics, which it maintained without unfolding at 100°C. Shortening and rigidification of loops in 2lvsN and 2lvsC and increased surface hydrogen bonds in 2lvsN were observed, as is common in thermophilic proteins. A buried disulfide and salt bridge in 2lvsN and 2lvsC, respectively, provided some stabilization, and addition of a homologous disulfide bond in EnHD slowed unfolding. The transferability and commonality of stabilization strategies among members of the three‐helix bundle fold suggest that these strategies may be general and deployable in designing thermostable proteins.
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Affiliation(s)
- Catrina Nguyen
- Department of Biology, Santa Clara University, Santa Clara, California, USA
| | - Lauren M Yearwood
- Department of Biology, Santa Clara University, Santa Clara, California, USA
| | - Michelle E McCully
- Department of Biology, Santa Clara University, Santa Clara, California, USA
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The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? Life (Basel) 2021; 11:life11080773. [PMID: 34440517 PMCID: PMC8398314 DOI: 10.3390/life11080773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.
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Fewer Exposed Lysine Residues May Explain Relative Resistance of Chicken Serum Albumin to In Vitro Protein Glycation in Comparison to Bovine Serum Albumin. J Mol Evol 2020; 88:653-661. [PMID: 32930811 DOI: 10.1007/s00239-020-09964-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 08/29/2020] [Indexed: 12/24/2022]
Abstract
Protein glycation and formation of advanced glycation end products is associated with several diseases resulting from high blood glucose concentrations. Plasma albumin is directly exposed to circulating glucose concentrations and is therefore at greater risk of glycation than hemoglobin. As plasma glucose concentrations in birds are 1.5-2 times higher than mammals of similar mass, avian albumin may be particularly at risk of glycation. Thus, the goal of the present study was to compare the in vitro formation of glycated albumin in chicken serum albumin (CSA) and bovine serum albumin (BSA) exposed to a range of glucose concentrations over a 16-week period. The level of glycation for CSA and BSA was quantified using boronate affinity columns to separate glycated albumin from non-glycated albumin and calculating the difference in protein concentration of each sample. The results indicate that CSA is glycated to a lesser degree than BSA when the albumins are exposed to increasing concentrations of glucose (38.8-500 mM). This was most apparent at week sixteen (500 mM glucose) where BSA expressed a higher degree of glycation (37.8 ± 0.76%) compared to CSA (19.7 ± 1.06%, P < 0.05). Additionally, percent glycation at week sixteen was significantly higher than the glucose-free solutions for both BSA and CSA, indicating that glycation is glucose-dependent. Analyses of the protein structures suggest that the relative resistance of CSA to glycation may be due to fewer lysine residues and variations in protein folding that shield more lysine residues from the plasma. Moreover, comparisons of reconstructed ancestral albumin sequences show that the ancestor of birds had 6-8 fewer lysine residues compared to that of mammals.
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Mohapatra SB, Manoj N. A conserved π-helix plays a key role in thermoadaptation of catalysis in the glycoside hydrolase family 4. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140523. [PMID: 32853774 DOI: 10.1016/j.bbapap.2020.140523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/21/2023]
Abstract
Here, we characterize the role of a π-helix in the molecular mechanisms underlying thermoadaptation in the glycoside hydrolase family 4 (GH4). The interspersed π-helix present in a subgroup is evolutionarily related to a conserved α-helix in other orthologs by a single residue insertion/deletion event. The insertional residue, Phe407, in a hyperthermophilic α-glucuronidase, makes specific interactions across the inter-subunit interface. In order to establish the sequence-structure-stability implications of the π-helix, the wild-type and the deletion variant (Δ407) were characterized. The variant showed a significant lowering of melting temperature and optimum temperature for the highest activity. Crystal structures of the proteins show a transformation of the π-helix to a continuous α-helix in the variant, identical to that in orthologs lacking this insertion. Thermodynamic parameters were determined from stability curves representing the temperature dependence of unfolding free energy. Though the proteins display maximum stabilities at similar temperatures, a higher melting temperature in the wild-type is achieved by a combination of higher enthalpy and lower heat capacity of unfolding. Comparisons of the structural changes, and the activity and thermodynamic profiles allow us to infer that specific non-covalent interactions, and the existence of residual structure in the unfolded state, are crucial determinants of its thermostability. These features permit the enzyme to balance the preservation of structure at a higher temperature with the thermodynamic stability required for optimum catalysis.
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Affiliation(s)
- Samar Bhallabha Mohapatra
- 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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Borges PT, Brissos V, Hernandez G, Masgrau L, Lucas MF, Monza E, Frazão C, Cordeiro TN, Martins LO. Methionine-Rich Loop of Multicopper Oxidase McoA Follows Open-to-Close Transitions with a Role in Enzyme Catalysis. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Guillem Hernandez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Laura Masgrau
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
- Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | - Emanuele Monza
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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12
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How Quickly Do Proteins Fold and Unfold, and What Structural Parameters Correlate with These Values? Biomolecules 2020; 10:biom10020197. [PMID: 32013136 PMCID: PMC7072309 DOI: 10.3390/biom10020197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/22/2020] [Accepted: 01/26/2020] [Indexed: 11/24/2022] Open
Abstract
The correlations between the logarithm of the unfolding rate of 108 proteins and their structural parameters were calculated. We showed that there is a good correlation between the logarithm of folding and unfolding rates (0.79) and protein stability and unfolding rate (0.79). Thus, the faster the protein folds, the faster it unfolds. Folding and unfolding rates are higher for the proteins with two-state kinetics, in comparison with the proteins with multi-state kinetics. At the same time, two-state bacterial proteins folds and unfolds two orders of magnitude faster than two-state eukaryotic proteins, and multi-state bacterial proteins folds and unfolds slower than multi-state eukaryotic proteins. Despite the fact that the folding rates of thermophilic and mesophilic proteins are close, the unfolding rates of thermophilic proteins is about two orders of magnitude lower than for mesophilic proteins. The correlation between unfolding rate and stability of thermophilic proteins is high (0.90). We also found that the unfolding rate correlates with such structural parameters as: size of the protein, radius of the cross-section, logarithm of absolute contact order, and radius of gyration. This information will be useful for engineering and designing new proteins with desired properties.
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Wang Y, Zhou Y, Shi S, Lu G, Lin X, Xie C, Liu D, Yao D. A rational design for improving the pepsin resistance of cellulase E4 isolated from T. fusca based on the evaluation of the transition complex and molecular structure. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles. Microorganisms 2019; 8:microorganisms8010059. [PMID: 31905784 PMCID: PMC7023208 DOI: 10.3390/microorganisms8010059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 11/25/2022] Open
Abstract
SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria.
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15
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Fang J. A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. Brief Bioinform 2019; 21:1285-1292. [PMID: 31273374 DOI: 10.1093/bib/bbz071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 01/02/2023] Open
Abstract
A number of machine learning (ML)-based algorithms have been proposed for predicting mutation-induced stability changes in proteins. In this critical review, we used hypothetical reverse mutations to evaluate the performance of five representative algorithms and found all of them suffer from the problem of overfitting. This approach is based on the fact that if a wild-type protein is more stable than a mutant protein, then the same mutant is less stable than the wild-type protein. We analyzed the underlying issues and suggest that the main causes of the overfitting problem include that the numbers of training cases were too small, and the features used in the models were not sufficiently informative for the task. We make recommendations on how to avoid overfitting in this important research area and improve the reliability and robustness of ML-based algorithms in general.
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Affiliation(s)
- Jianwen Fang
- Computational & Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA
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16
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Disulfide bonds elimination of endoglucanase II from Trichoderma reesei by site-directed mutagenesis to improve enzyme activity and thermal stability: An experimental and theoretical approach. Int J Biol Macromol 2018; 120:1572-1580. [DOI: 10.1016/j.ijbiomac.2018.09.164] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 09/23/2018] [Accepted: 09/25/2018] [Indexed: 01/21/2023]
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17
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Marginal protein stability drives subcellular proteome isoelectric point. Proc Natl Acad Sci U S A 2018; 115:11778-11783. [PMID: 30385634 DOI: 10.1073/pnas.1809098115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome-a highly acidic compartment in the cell-have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.
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18
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Finch AJ, Kim JR. Thermophilic Proteins as Versatile Scaffolds for Protein Engineering. Microorganisms 2018; 6:microorganisms6040097. [PMID: 30257429 PMCID: PMC6313779 DOI: 10.3390/microorganisms6040097] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 09/23/2018] [Accepted: 09/23/2018] [Indexed: 01/18/2023] Open
Abstract
Literature from the past two decades has outlined the existence of a trade-off between protein stability and function. This trade-off creates a unique challenge for protein engineers who seek to introduce new functionality to proteins. These engineers must carefully balance the mutation-mediated creation and/or optimization of function with the destabilizing effect of those mutations. Subsequent research has shown that protein stability is positively correlated with "evolvability" or the ability to support mutations which bestow new functionality on the protein. Since the ultimate goal of protein engineering is to create and/or optimize a protein's function, highly stable proteins are preferred as potential scaffolds for protein engineering. This review focuses on the application potential for thermophilic proteins as scaffolds for protein engineering. The relatively high inherent thermostability of these proteins grants them a great deal of mutational robustness, making them promising scaffolds for various protein engineering applications. Comparative studies on the evolvability of thermophilic and mesophilic proteins have strongly supported the argument that thermophilic proteins are more evolvable than mesophilic proteins. These findings indicate that thermophilic proteins may represent the scaffold of choice for protein engineering in the future.
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Affiliation(s)
- Anthony J Finch
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA.
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19
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A novel strategy to improve the thermostability of Penicillium camembertii mono- and di-acylglycerol lipase. Biochem Biophys Res Commun 2018; 500:639-644. [DOI: 10.1016/j.bbrc.2018.04.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 04/14/2018] [Indexed: 01/24/2023]
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20
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Fontanillas E, Galzitskaya OV, Lecompte O, Lobanov MY, Tanguy A, Mary J, Girguis PR, Hourdez S, Jollivet D. Proteome Evolution of Deep-Sea Hydrothermal Vent Alvinellid Polychaetes Supports the Ancestry of Thermophily and Subsequent Adaptation to Cold in Some Lineages. Genome Biol Evol 2017; 9:279-296. [PMID: 28082607 PMCID: PMC5381640 DOI: 10.1093/gbe/evw298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2016] [Indexed: 12/22/2022] Open
Abstract
Temperature, perhaps more than any other environmental factor, is likely to influence the evolution of all organisms. It is also a very interesting factor to understand how genomes are shaped by selection over evolutionary timescales, as it potentially affects the whole genome. Among thermophilic prokaryotes, temperature affects both codon usage and protein composition to increase the stability of the transcriptional/translational machinery, and the resulting proteins need to be functional at high temperatures. Among eukaryotes less is known about genome evolution, and the tube-dwelling worms of the family Alvinellidae represent an excellent opportunity to test hypotheses about the emergence of thermophily in ectothermic metazoans. The Alvinellidae are a group of worms that experience varying thermal regimes, presumably having evolved into these niches over evolutionary times. Here we analyzed 423 putative orthologous loci derived from 6 alvinellid species including the thermophilic Alvinella pompejana and Paralvinella sulfincola. This comparative approach allowed us to assess amino acid composition, codon usage, divergence, direction of residue changes and the strength of selection along the alvinellid phylogeny, and to design a new eukaryotic thermophilic criterion based on significant differences in the residue composition of proteins. Contrary to expectations, the alvinellid ancestor of all present-day species seems to have been thermophilic, a trait subsequently maintained by purifying selection in lineages that still inhabit higher temperature environments. In contrast, lineages currently living in colder habitats likely evolved under selective relaxation, with some degree of positive selection for low-temperature adaptation at the protein level.
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Affiliation(s)
- Eric Fontanillas
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| | - Oxana V Galzitskaya
- Laboratory of Protein Physics, Institute of Protein Research, RAS, Institutskaya street, 4, 142290 Pushchino, Moscow, Russia
| | - Odile Lecompte
- CSTB - ICUBE, UMR7357, Faculté de Médecine, 4 rue Kirschleger, 67085 Strasbourg, France
| | - Mikhail Y Lobanov
- Laboratory of Protein Physics, Institute of Protein Research, RAS, Institutskaya street, 4, 142290 Pushchino, Moscow, Russia
| | - Arnaud Tanguy
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| | - Jean Mary
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| | - Peter R Girguis
- Department of Organismic & Evolutionary Biology, Harvard University Biological Laboratories, Cambridge, MA
| | - Stéphane Hourdez
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
| | - Didier Jollivet
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France
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21
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Geertz-Hansen HM, Kiemer L, Nielsen M, Stanchev K, Blom N, Brunak S, Petersen TN. Protein features as determinants of wild-type glycoside hydrolase thermostability. Proteins 2017; 85:2036-2044. [DOI: 10.1002/prot.25357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Henrik Marcus Geertz-Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; DK-2800 Lyngby Denmark
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Novozymes A/S; DK-2880 Bagsvaerd Denmark
| | | | - Morten Nielsen
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin, San Martin, B 1650 HMP; Buenos Aires Argentina
| | - Kiril Stanchev
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
| | - Nikolaj Blom
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; DK-2800 Lyngby Denmark
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Faculty of Health and Medical Sciences; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen; DK-2200 Copenhagen N Denmark
| | - Thomas Nordahl Petersen
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
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22
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Medvedev KE, Kolchanov NA, Afonnikov DA. Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions. J Bioinform Comput Biol 2017; 15:1650036. [DOI: 10.1142/s0219720016500360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The understanding of biological and molecular mechanisms providing survival of cells under extreme temperatures and pressures will help to answer fundamental questions related to the origin of life and to design of biotechnologically important enzymes with new properties. Here, we analyze amino acid sequences of the Nip7 proteins from 35 archaeal species to identify positions containing mutations specific to the hydrostatic pressure and temperature of organism’s habitat. The number of such positions related to pressure change is much lower than related to temperature change. The results suggest that adaptation to temperature changes of the Nip7 protein cause more pronounced modifications in sequence and structure, than to the pressure changes. Structural analysis of residues at these positions demonstrated their involvement in salt-bridge formation, which may reflect the importance of protein structure stabilization by salt-bridges at extreme environmental conditions.
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Affiliation(s)
- Kirill E. Medvedev
- Department of Biophysics, University of Texas Southwestern, Medical Center, Dallas, Texas 75390, USA
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl., 1, Moscow 123182, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
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23
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Leng F, Xu C, Xia XY, Pan XM. Establishing knowledge on the sequence arrangement pattern of nucleated protein folding. PLoS One 2017; 12:e0173583. [PMID: 28273143 PMCID: PMC5342263 DOI: 10.1371/journal.pone.0173583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/22/2017] [Indexed: 11/21/2022] Open
Abstract
The heat-tolerance mechanisms of (hyper)thermophilic proteins provide a unique opportunity to investigate the unsolved protein folding problem. In an attempt to determine whether the interval between residues in sequence might play a role in determining thermostability, we constructed a sequence interval-dependent value function to calculate the residue pair frequency. Additionally, we identified a new sequence arrangement pattern, where like-charged residues tend to be adjacently assembled, while unlike-charged residues are distributed over longer intervals, using statistical analysis of a large sequence database. This finding indicated that increasing the intervals between unlike-charged residues can increase protein thermostability, with the arrangement patterns of these charged residues serving as thermodynamically favorable nucleation points for protein folding. Additionally, we identified that the residue pairs K-E, R-E, L-V and V-V involving long sequence intervals play important roles involving increased protein thermostability. This work demonstrated a novel approach for considering sequence intervals as keys to understanding protein folding. Our findings of novel relationships between residue arrangement and protein thermostability can be used in industry and academia to aid the design of thermostable proteins.
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Affiliation(s)
- Fei Leng
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chao Xu
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xia-Yu Xia
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xian-Ming Pan
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail:
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24
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Point mutation Gln121-Arg increased temperature optima of Bacillus lipase (1.4 subfamily) by fifteen degrees. Int J Biol Macromol 2016; 88:507-14. [DOI: 10.1016/j.ijbiomac.2016.04.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/14/2016] [Accepted: 04/10/2016] [Indexed: 11/18/2022]
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25
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HU histone-like DNA-binding protein from Thermus thermophilus: structural and evolutionary analyses. Extremophiles 2016; 20:695-709. [DOI: 10.1007/s00792-016-0859-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
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26
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Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins. J Mol Graph Model 2016; 64:85-93. [DOI: 10.1016/j.jmgm.2016.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/03/2016] [Indexed: 11/21/2022]
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27
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Qiu Y, Wu X, Xie C, Hu Y, Liu D, Ma Y, Yao D. A rational design for improving the trypsin resistance of aflatoxin-detoxifizyme (ADTZ) based on molecular structure evaluation. Enzyme Microb Technol 2016; 86:84-92. [PMID: 26992797 DOI: 10.1016/j.enzmictec.2016.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 01/26/2016] [Accepted: 02/12/2016] [Indexed: 12/01/2022]
Abstract
The resistance of feed enzymes against proteases is crucial in livestock farming. In this study, the trypsin resistance of aflatoxin-detoxifizyme (ADTZ) is improved. ADTZ possesses 72 lys/arg residue sites, 45 of which are scattered on the outermost layers of the molecule (RSA≧25%). These 45 lys/arg sites could be target sites for trypsin hydrolysis. By considering shape-matching (including physical and secondary bond interactions) and the "induced fit-effect", we hypothesized that some of these lys/arg sites are vulnerable to trypsin. A protein-protein docking simulation method was used to avoid the massive computational requirements and to address the intricacy of selecting candidate sites, as candidate site selection is affected by space displacement. Optimal mutants (K244Q/K213C/K270T and R356E/K357T/R623C) were predicted by computational design with protein folding energy analysis and molecular dynamics simulations. A trypsin digestion assay was performed, and the mutants displayed much higher stability against trypsin hydrolysis compared to the native enzyme. Moreover, temperature- and pH-activity profiles revealed that the designed mutations did not affect the catalytic activity of the enzyme.
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Affiliation(s)
- Yuxin Qiu
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province 510632, China
| | - Xiyang Wu
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province 510632, China
| | - Chunfang Xie
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province 510632, China
| | - Yadong Hu
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province 510632, China
| | - Daling Liu
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province 510632, China
| | - Yi Ma
- National Engineering Research Center of Genetic Medicine, Guangzhou City, Guangdong Province 510632, China
| | - Dongsheng Yao
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou City, Guangdong Province 510632, China.
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28
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Kim H, Kim S, Jung Y, Han J, Yun JH, Chang I, Lee W. Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880. PLoS One 2016; 11:e0145853. [PMID: 26766214 PMCID: PMC4713090 DOI: 10.1371/journal.pone.0145853] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
The folding mechanism of typical proteins has been studied widely, while our understanding of the origin of the high stability of thermophilic proteins is still elusive. Of particular interest is how an atypical thermophilic protein with a novel fold maintains its structure and stability under extreme conditions. Folding-unfolding transitions of MTH1880, a thermophilic protein from Methanobacterium thermoautotrophicum, induced by heat, urea, and GdnHCl, were investigated using spectroscopic techniques including circular dichorism, fluorescence, NMR combined with molecular dynamics (MD) simulations. Our results suggest that MTH1880 undergoes a two-state N to D transition and it is extremely stable against temperature and denaturants. The reversibility of refolding was confirmed by spectroscopic methods and size exclusion chromatography. We found that the hyper-stability of the thermophilic MTH1880 protein originates from an extensive network of both electrostatic and hydrophobic interactions coordinated by the central β-sheet. Spectroscopic measurements, in combination with computational simulations, have helped to clarify the thermodynamic and structural basis for hyper-stability of the novel thermophilic protein MTH1880.
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Affiliation(s)
- Heeyoun Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Sangyeol Kim
- Department of Physics, Pusan National University, Busan, 609–735, Korea
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
| | - Youngjin Jung
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Jeongmin Han
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Ji-Hye Yun
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 711–873, Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
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29
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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30
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Yang LL, Tang SK, Huang Y, Zhi XY. Low Temperature Adaptation Is Not the Opposite Process of High Temperature Adaptation in Terms of Changes in Amino Acid Composition. Genome Biol Evol 2015; 7:3426-33. [PMID: 26614525 PMCID: PMC4700962 DOI: 10.1093/gbe/evv232] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Previous studies focused on psychrophilic adaptation generally have demonstrated that multiple mechanisms work together to increase protein flexibility and activity, as well as to decrease the thermostability of proteins. However, the relationship between high and low temperature adaptations remains unclear. To investigate this issue, we collected the available predicted whole proteome sequences of species with different optimal growth temperatures, and analyzed amino acid variations and substitutional asymmetry in pairs of homologous proteins from related species. We found that changes in amino acid composition associated with low temperature adaptation did not exhibit a coherent opposite trend when compared with changes in amino acid composition associated with high temperature adaptation. This result indicates that during their evolutionary histories the proteome-scale evolutionary patterns associated with prokaryotes exposed to low temperature environments were distinct from the proteome-scale evolutionary patterns associated with prokaryotes exposed to high temperature environments in terms of changes in amino acid composition of the proteins.
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Affiliation(s)
- Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Shu-Kun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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31
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Supek F. The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function. J Mol Evol 2015; 82:65-73. [PMID: 26538122 DOI: 10.1007/s00239-015-9714-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/30/2015] [Indexed: 02/07/2023]
Abstract
Some mutations in gene coding regions exchange one synonymous codon for another, and thus do not alter the amino acid sequence of the encoded protein. Even though they are often called 'silent,' these mutations may exhibit a plethora of effects on the living cell. Therefore, they are often selected during evolution, causing synonymous codon usage biases in genomes. Comparative analyses of bacterial, archaeal, fungal, and human cancer genomes have found many links between a gene's biological role and the accrual of synonymous mutations during evolution. In particular, highly expressed genes in certain functional categories are enriched with optimal codons, which are decoded by the abundant tRNAs, thus enhancing the speed and accuracy of the translating ribosome. The set of genes exhibiting codon adaptation differs between genomes, and these differences show robust associations to organismal phenotypes. In addition to selection for translation efficiency, other distinct codon bias patterns have been found in: amino acid starvation genes, cyclically expressed genes, tissue-specific genes in animals and plants, oxidative stress response genes, cellular differentiation genes, and oncogenes. In addition, genomes of organisms harboring tRNA modifications exhibit particular codon preferences. The evolutionary trace of codon bias patterns across orthologous genes may be examined to learn about a gene's relevance to various phenotypes, or, more generally, its function in the cell.
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Affiliation(s)
- Fran Supek
- Division of electronics, Rudjer Boskovic Institute, 10000, Zagreb, Croatia.
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
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32
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Meysman P, Zhou C, Cule B, Goethals B, Laukens K. Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns. BioData Min 2015; 8:4. [PMID: 25657820 PMCID: PMC4318390 DOI: 10.1186/s13040-015-0038-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 01/18/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The three-dimensional structure of a protein is an essential aspect of its functionality. Despite the large diversity in protein structures and functionality, it is known that there are common patterns and preferences in the contacts between amino acid residues, or between residues and other biomolecules, such as DNA. The discovery and characterization of these patterns is an important research topic within structural biology as it can give fundamental insight into protein structures and can aid in the prediction of unknown structures. RESULTS Here we apply an efficient spatial pattern miner to search for sets of amino acids that occur frequently in close spatial proximity in the protein structures of the Protein DataBank. This allowed us to mine for a new class of amino acid patterns, that we term FreSCOs (Frequent Spatially Cohesive Component sets), which feature synergetic combinations. To demonstrate the relevance of these FreSCOs, they were compared in relation to the thermostability of the protein structure and the interaction preferences of DNA-protein complexes. In both cases, the results matched well with prior investigations using more complex methods on smaller data sets. CONCLUSIONS The currently characterized protein structures feature a diverse set of frequent amino acid patterns that can be related to the stability of the protein molecular structure and that are independent from protein function or specific conserved domains.
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Affiliation(s)
- Pieter Meysman
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Cheng Zhou
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Boris Cule
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Bart Goethals
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
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33
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Goncearenco A, Berezovsky IN. The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins. Biol Direct 2014; 9:29. [PMID: 25496919 PMCID: PMC4273451 DOI: 10.1186/s13062-014-0029-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/01/2014] [Indexed: 11/26/2022] Open
Abstract
Background Mutations in nucleotide sequences provide a foundation for genetic variability, and selection is the driving force of the evolution and molecular adaptation. Despite considerable progress in the understanding of selective forces and their compositional determinants, the very nature of underlying mutational biases remains unclear. Results We explore here a fundamental tradeoff, which analytically describes mutual adjustment of the nucleotide and amino acid compositions and its possible effect on the mutational biases. The tradeoff is determined by the interplay between the genetic code, optimization of the codon entropy, and demands on the structure and stability of nucleic acids and proteins. Conclusion The tradeoff is the unifying property of all prokaryotes regardless of the differences in their phylogenies, life styles, and extreme environments. It underlies mutational biases characteristic for genomes with different nucleotide and amino acid compositions, providing foundation for evolution and adaptation. Reviewers This article was reviewed by Eugene Koonin, Michael Gromiha, and Alexander Schleiffer. Electronic supplementary material The online version of this article (doi:10.1186/s13062-014-0029-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Goncearenco
- Computational Biology Unit and Department of Informatics, University of Bergen, N-5008, Bergen, Norway. .,Current address: Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, USA.
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore. .,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117597, Singapore, Singapore.
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Frappier V, Najmanovich R. Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering. Protein Sci 2014; 24:474-83. [PMID: 25367089 DOI: 10.1002/pro.2592] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 11/10/2022]
Abstract
We recently introduced ENCoM, an elastic network atomic contact model, as the first coarse-grained normal mode analysis method that accounts for the nature of amino acids and can predict the effect of mutations on thermostability based on changes vibrational entropy. In this proof-of-concept article, we use pairs of mesophile and thermophile homolog proteins with identical structures to determine if a measure of vibrational entropy based on normal mode analysis can discriminate thermophile from mesophile proteins. We observe that in around 60% of cases, thermophile proteins are more rigid at equivalent temperatures than their mesophile counterpart and this difference can guide the design of proteins to increase their thermostability through series of mutations. We observe that mutations separating thermophile proteins from their mesophile orthologs contribute independently to a decrease in vibrational entropy and discuss the application and implications of this methodology to protein engineering.
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Affiliation(s)
- Vincent Frappier
- Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, J1H 5N4, Quebec, Canada
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35
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Prediction of the determinants of thermal stability by linear discriminant analysis: the case of the glutamate dehydrogenase protein family. J Theor Biol 2014; 357:160-8. [PMID: 24853273 DOI: 10.1016/j.jtbi.2014.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 11/21/2022]
Abstract
Little is known about the determinants of thermal stability in individual protein families. Most of the knowledge on thermostability comes, in fact, from comparative analyses between large, and heterogeneous, sets of thermo- and mesophilic proteins. Here, we present a multivariate statistical approach aimed to detect signature sequences for thermostability in a single protein family. It was applied to the glutamate dehydrogenase (GDH) family, which is a good model for investigating this peculiar process. The structure of GDH consists of six subunits, each of them organized into two domains. Formation of ion-pair networks on the surface of the protein subunits, or increase in the inter-subunit hydrophobic interactions, have been suggested as important factors for explaining stability at high temperatures. However, identification of the amino acid changes that are involved in this process still remains elusive. Our approach consisted of a linear discriminant analysis on a set of GDH sequences from Archaea and Bacteria (33 thermo- and 36 mesophilic GDHs). It led to detection of 3 amino acid clusters as the putative determinants of thermal stability. They were localized at the subunit interface or in close proximity to the binding site of the NAD(P)(+) coenzyme. Analysis within the clusters led to prediction of 8 critical amino acid sites. This approach could have a wide utility, in the ligth of the notion that each protein family seems to adopt its own strategy for achieving thermostability.
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36
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Mills BJ, Laurence JS. Stability analysis of an inline peptide-based conjugate for metal delivery: nickel(II)-claMP Tag epidermal growth factor as a model system. J Pharm Sci 2014; 104:416-23. [PMID: 25212829 DOI: 10.1002/jps.24132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/11/2014] [Accepted: 07/30/2014] [Indexed: 01/25/2023]
Abstract
Metals are a key component of many diagnostic imaging and biotechnology applications, and the majority of cancer patients receive a platinum-based drug as part of their treatment. Significant effort has been devoted to developing tight binding synthetic chelators to enable effective targeted delivery of metal-based conjugates, with most successes involving lanthanides rather than transition metals for diagnostic imaging. Chemical conjugation modifies the protein's properties and generates a heterogeneous mixture of products. Chelator attachment is typically carried out by converting the amino group on lysines to an amide, which can impact the stability and solubility of the targeting protein and these properties vary among the set of individual conjugate species. Site-specific attachment is sought to reduce complexity and control stability. Here, the metal abstraction peptide technology was applied to create the claMP Tag, an inline platform for generating site-specific conjugates involving transition metals. The claMP Tag was genetically encoded into epidermal growth factor (EGF) and loaded with nickel(II) as a model system to demonstrate that the tag within the homogeneous inline conjugate presents sufficient solution stability to enable biotechnology applications. The structure and disulfide network of the protein and chemical stability of the claMP Tag and EGF components were characterized.
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Affiliation(s)
- Brittney J Mills
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, 66045
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37
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Turner KB, Zabetakis D, Goldman ER, Anderson GP. Enhanced stabilization of a stable single domain antibody for SEB toxin by random mutagenesis and stringent selection. Protein Eng Des Sel 2014; 27:89-95. [PMID: 24488977 DOI: 10.1093/protein/gzu001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Single domain antibodies, recombinant variable heavy domains derived from the unique heavy-chain only antibodies found in camelids and sharks, are exceptionally rugged due to their ability to refold following heat or chemical denaturation. In addition, a number of single domain antibodies have been found to possess high melting points which provide an even greater degree of stability; one of these, llama-derived A3, is a binder of Staphylococcal enterotoxin B and has a Tm of 83.5 °C. In this work, we utilized random mutagenesis and stringent selection in an effort to obtain variants of A3 with even higher melting points. This effort resulted in the selection of a double mutant, A3-T28I-S72I, which has a melting point of 90.0 °C and near wild-type affinity for the target antigen. We further characterized the mutations individually to determine that while both contributed to the thermal stabilization, the T28I mutation accounted for ∼ 4.1 °C of the 6.5 °C increase. This work demonstrates that by the addition of relatively subtle changes it is possible to further improve the melting temperature of single domain antibodies that are already remarkably stable.
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Affiliation(s)
- Kendrick B Turner
- American Society for Engineering Education Postdoctoral Fellow, Naval Research Laboratory, Washington, DC 20375, USA
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38
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Rathi PC, Höffken HW, Gohlke H. Quality matters: extension of clusters of residues with good hydrophobic contacts stabilize (hyper)thermophilic proteins. J Chem Inf Model 2014; 54:355-61. [PMID: 24437522 PMCID: PMC3985445 DOI: 10.1021/ci400568c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Identifying determinant(s) of protein thermostability is key for rational and data-driven protein engineering. By analyzing more than 130 pairs of mesophilic/(hyper)thermophilic proteins, we identified the quality (residue-wise energy) of hydrophobic interactions as a key factor for protein thermostability. This distinguishes our study from previous ones that investigated predominantly structural determinants. Considering this key factor, we successfully discriminated between pairs of mesophilic/(hyper)thermophilic proteins (discrimination accuracy: ∼80%) and searched for structural weak spots in E. coli dihydrofolate reductase (classification accuracy: 70%).
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Affiliation(s)
- Prakash Chandra Rathi
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich Heine University , Universitätsstr. 1, 40225 Düsseldorf, Germany
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39
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Goncearenco A, Ma BG, Berezovsky IN. Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins. Nucleic Acids Res 2013; 42:2879-92. [PMID: 24371267 PMCID: PMC3950714 DOI: 10.1093/nar/gkt1336] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.
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Affiliation(s)
- Alexander Goncearenco
- CBU, University of Bergen, 5020 Bergen, Norway, Department of Informatics, University of Bergen, 5020 Bergen, Norway, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671 Singapore and Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
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40
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Yennamalli RM, Rader AJ, Kenny AJ, Wolt JD, Sen TZ. Endoglucanases: insights into thermostability for biofuel applications. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:136. [PMID: 24070146 PMCID: PMC3856469 DOI: 10.1186/1754-6834-6-136] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/24/2013] [Indexed: 05/03/2023]
Abstract
Obtaining bioethanol from cellulosic biomass involves numerous steps, among which the enzymatic conversion of the polymer to individual sugar units has been a main focus of the biotechnology industry. Among the cellulases that break down the polymeric cellulose are endoglucanases that act synergistically for subsequent hydrolytic reactions. The endoglucanases that have garnered relatively more attention are those that can withstand high temperatures, i.e., are thermostable. Although our understanding of thermostability in endoglucanases is incomplete, some molecular features that are responsible for increased thermostability have been recently identified. This review focuses on the investigations of endoglucanases and their implications for biofuel applications.
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Affiliation(s)
- Ragothaman M Yennamalli
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames 50011, IA, USA
- Present Address: Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
| | - Andrew J Rader
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis 46202, IN, USA
- Present Address: State Farm Insurance, Indianapolis 46240, IN, USA
| | - Adam J Kenny
- Biosafety Institute for Genetically Modified Agricultural Products and Department of Agronomy, Iowa State University, Ames 50011, IA, USA
- Present Address: Brownells, Inc, Montezuma, IA 50171, USA
| | - Jeffrey D Wolt
- Biosafety Institute for Genetically Modified Agricultural Products and Department of Agronomy, Iowa State University, Ames 50011, IA, USA
| | - Taner Z Sen
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames 50011, IA, USA
- Bioinformatics and Computational Biology Program, Iowa State University, Ames 50011, IA, USA
- 1025 Crop Genome Informatics Lab, Iowa State University, Ames 50011, IA, USA
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41
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Takano K, Aoi A, Koga Y, Kanaya S. Evolvability of Thermophilic Proteins from Archaea and Bacteria. Biochemistry 2013; 52:4774-80. [DOI: 10.1021/bi400652c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo,
Sakyo-ku, Kyoto 606-8522, Japan
| | - Atsushi Aoi
- Department of Material and Life
Science, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Yuichi Koga
- Department of Material and Life
Science, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Shigenori Kanaya
- Department of Material and Life
Science, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
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42
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Mamonova TB, Glyakina AV, Galzitskaya OV, Kurnikova MG. Stability and rigidity/flexibility-two sides of the same coin? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:854-66. [PMID: 23416444 DOI: 10.1016/j.bbapap.2013.02.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 12/21/2012] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Protein molecules require both flexibility and rigidity for functioning. The fast and accurate prediction of protein rigidity/flexibility is one of the important problems in protein science. We have determined flexible regions for four homologous pairs from thermophilic and mesophilic organisms by two methods: the fast FoldUnfold which uses amino acid sequence and the time consuming MDFirst which uses three-dimensional structures. We demonstrate that both methods allow determining flexible regions in protein structure. For three of the four thermophile-mesophile pairs of proteins, FoldUnfold predicts practically the same flexible regions which have been found by the MD/First method. As expected, molecular dynamics simulations show that thermophilic proteins are more rigid in comparison to their mesophilic homologues. Analysis of rigid clusters and their decomposition provides new insights into protein stability. It has been found that the local networks of salt bridges and hydrogen bonds in thermophiles render their structure more stable with respect to fluctuations of individual contacts. Such network includes salt bridge triads Agr-Glu-Lys and Arg-Glu-Arg, or salt bridges (such as Arg-Glu) connected with hydrogen bonds. This ionic network connects alpha helices and rigidifies the structure. Mesophiles can be characterized by stand alone salt bridges and hydrogen bonds or small ionic clusters. Such difference in the network of salt bridges results in different flexibility of homologous proteins. Combining both approaches allows characterizing structural features in atomic detail that determine the rigidity/flexibility of a protein structure. This article is a part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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Affiliation(s)
- Tatyana B Mamonova
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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43
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Gromiha MM, Pathak MC, Saraboji K, Ortlund EA, Gaucher EA. Hydrophobic environment is a key factor for the stability of thermophilic proteins. Proteins 2013; 81:715-21. [PMID: 23319168 DOI: 10.1002/prot.24232] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/16/2012] [Accepted: 11/28/2012] [Indexed: 11/07/2022]
Affiliation(s)
- M Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India.
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44
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Li Y, Fang J. PROTS-RF: a robust model for predicting mutation-induced protein stability changes. PLoS One 2012; 7:e47247. [PMID: 23077576 PMCID: PMC3471942 DOI: 10.1371/journal.pone.0047247] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022] Open
Abstract
The ability to improve protein thermostability via protein engineering is of great scientific interest and also has significant practical value. In this report we present PROTS-RF, a robust model based on the Random Forest algorithm capable of predicting thermostability changes induced by not only single-, but also double- or multiple-point mutations. The model is built using 41 features including evolutionary information, secondary structure, solvent accessibility and a set of fragment-based features. It achieves accuracies of 0.799,0.782, 0.787, and areas under receiver operating characteristic (ROC) curves of 0.873, 0.868 and 0.862 for single-, double- and multiple- point mutation datasets, respectively. Contrary to previous suggestions, our results clearly demonstrate that a robust predictive model trained for predicting single point mutation induced thermostability changes can be capable of predicting double and multiple point mutations. It also shows high levels of robustness in the tests using hypothetical reverse mutations. We demonstrate that testing datasets created based on physical principles can be highly useful for testing the robustness of predictive models.
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Affiliation(s)
- Yunqi Li
- Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, Kansas, United States of America
| | - Jianwen Fang
- Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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45
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Jollivet D, Mary J, Gagnière N, Tanguy A, Fontanillas E, Boutet I, Hourdez S, Segurens B, Weissenbach J, Poch O, Lecompte O. Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm. PLoS One 2012; 7:e31150. [PMID: 22348046 PMCID: PMC3277501 DOI: 10.1371/journal.pone.0031150] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 01/03/2012] [Indexed: 12/19/2022] Open
Abstract
Taking advantage of the massive genome sequencing effort made on thermophilic prokaryotes, thermal adaptation has been extensively studied by analysing amino acid replacements and codon usage in these unicellular organisms. In most cases, adaptation to thermophily is associated with greater residue hydrophobicity and more charged residues. Both of these characteristics are positively correlated with the optimal growth temperature of prokaryotes. In contrast, little information has been collected on the molecular 'adaptive' strategy of thermophilic eukaryotes. The Pompeii worm A. pompejana, whose transcriptome has recently been sequenced, is currently considered as the most thermotolerant eukaryote on Earth, withstanding the greatest thermal and chemical ranges known. We investigated the amino-acid composition bias of ribosomal proteins in the Pompeii worm when compared to other lophotrochozoans and checked for putative adaptive changes during the course of evolution using codon-based Maximum likelihood analyses. We then provided a comparative analysis of codon usage and amino-acid replacements from a greater set of orthologous genes between the Pompeii worm and Paralvinella grasslei, one of its closest relatives living in a much cooler habitat. Analyses reveal that both species display the same high GC-biased codon usage and amino-acid patterns favoring both positively-charged residues and protein hydrophobicity. These patterns may be indicative of an ancestral adaptation to the deep sea and/or thermophily. In addition, the Pompeii worm displays a set of amino-acid change patterns that may explain its greater thermotolerance, with a significant increase in Tyr, Lys and Ala against Val, Met and Gly. Present results indicate that, together with a high content in charged residues, greater proportion of smaller aliphatic residues, and especially alanine, may be a different path for metazoans to face relatively 'high' temperatures and thus a novelty in thermophilic metazoans.
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Affiliation(s)
- Didier Jollivet
- Adaptation & Diversité en Milieu Marin, CNRS UMR 7144, Roscoff, France.
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46
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Thangakani AM, Kumar S, Velmurugan D, Gromiha MSM. How do thermophilic proteins resist aggregation? Proteins 2012; 80:1003-15. [DOI: 10.1002/prot.24002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 11/18/2011] [Accepted: 11/21/2011] [Indexed: 11/08/2022]
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47
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Hsieh D, Davis A, Nanda V. A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding. Protein Sci 2011; 21:50-62. [PMID: 22031179 DOI: 10.1002/pro.758] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 09/06/2011] [Accepted: 10/19/2011] [Indexed: 12/16/2022]
Abstract
Outer membrane β-barrel proteins differ from α-helical inner membrane proteins in lipid environment, secondary structure, and the proposed processes of folding and insertion. It is reasonable to expect that outer membrane proteins may contain primary sequence information specific for their folding and insertion behavior. In previous work, a depth-dependent insertion potential, E(z) , was derived for α-helical inner membrane proteins. We have generated an equivalent potential for TM β-barrel proteins. The similarities and differences between these two potentials provide insight into unique aspects of the folding and insertion of β-barrel membrane proteins. This potential can predict orientation within the membrane and identify functional residues involved in intermolecular interactions.
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Affiliation(s)
- Daniel Hsieh
- BioMaPS Institute and the Graduate Program in Computational Biology and Molecular Biophysics, Rutgers University, Piscataway, NJ 08854, USA
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48
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Li Y, Zhang J, Tai D, Middaugh CR, Zhang Y, Fang J. PROTS: a fragment based protein thermo-stability potential. Proteins 2011; 80:81-92. [PMID: 21976375 DOI: 10.1002/prot.23163] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/18/2011] [Accepted: 07/31/2011] [Indexed: 12/30/2022]
Abstract
Designing proteins with enhanced thermo-stability has been a main focus of protein engineering because of its theoretical and practical significance. Despite extensive studies in the past years, a general strategy for stabilizing proteins still remains elusive. Thus effective and robust computational algorithms for designing thermo-stable proteins are in critical demand. Here we report PROTS, a sequential and structural four-residue fragment based protein thermo-stability potential. PROTS is derived from a nonredundant representative collection of thousands of thermophilic and mesophilic protein structures and a large set of point mutations with experimentally determined changes of melting temperatures. To the best of our knowledge, PROTS is the first protein stability predictor based on integrated analysis and mining of these two types of data. Besides conventional cross validation and blind testing, we introduce hypothetical reverse mutations as a means of testing the robustness of protein thermo-stability predictors. In all tests, PROTS demonstrates the ability to reliably predict mutation induced thermo-stability changes as well as classify thermophilic and mesophilic proteins. In addition, this white-box predictor allows easy interpretation of the factors that influence mutation induced protein stability changes at the residue level.
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Affiliation(s)
- Yunqi Li
- Applied Bioinformatics Laboratory, the University of Kansas, Lawrence, Kansas 66047, USA
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49
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Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C, Moisan MC, Henrissat B, Coutinho PM, Lombard V, Natvig DO, Lindquist E, Schmutz J, Lucas S, Harris P, Powlowski J, Bellemare A, Taylor D, Butler G, de Vries RP, Allijn IE, van den Brink J, Ushinsky S, Storms R, Powell AJ, Paulsen IT, Elbourne LDH, Baker SE, Magnuson J, Laboissiere S, Clutterbuck AJ, Martinez D, Wogulis M, de Leon AL, Rey MW, Tsang A. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnol 2011; 29:922-7. [PMID: 21964414 DOI: 10.1038/nbt.1976] [Citation(s) in RCA: 305] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 08/18/2011] [Indexed: 11/09/2022]
Abstract
Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.
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50
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Gorania M, Seker H, Haris PI. Predicting a protein's melting temperature from its amino acid sequence. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2011; 2010:1820-3. [PMID: 21095941 DOI: 10.1109/iembs.2010.5626421] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Melting temperature is an important characteristic feature of a protein and is used for various purposes such as in drug development. Currently protein melting temperature is determined by laboratory methods such as Differential Scanning Calorimetry, Circular Dichroism, Fourier transform infrared spectroscopy and several other methods. These methods are laborious and costly. Therefore, we propose a novel bioinformatics based method for predicting protein melting temperature from amino acid sequence of a protein. This is not only a challenging task but has been previously unexplored. For this study, melting temperature of 230 proteins from a range of organisms was collected along with their sequence information from the published literature. The melting temperature of these proteins represents a very large spectrum and varies between 25°C and 113°C. The protein sequences are then used to derive two sets of sequence-driven features, namely amino acid composition (AAC) and pseudo-amino acid composition (PseudoAAC) to characterise the proteins. In order to predict the melting temperature, two different computational intelligence methods, namely artificial neural networks (ANN) and adaptive network-fuzzy inference system (ANFIS) were utilized. Amongst over 100 different models generated, the ANN produced the best model with the least error (0.01087 for the AAC and 0.01086 for the pseudoAAC). As both feature sets yielded quite similar error and computation of pseudoAAC is costly when compared to that of AAC, traditional AAC seems to be an effective feature set for predicting melting temperature. The results obtained in this study are very promising and, for the first time, shows that the melting temperature of a protein can be predicted from its amino acid sequence only. Therefore, costly lab-based experiments may not be required to measure the melting temperature and the bioinformatics models can help speed up laboratory processes such as in drug development.
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Affiliation(s)
- Malde Gorania
- Bio-Health Informatics Research Group at the Centre of Computational, Department of Informatics, Faculty of Technology, De Montfort University, UK LE11 9BH.
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