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Kumar J, Jyotisha, Qureshi R, Jagruthi P, Arifuddin M, Qureshi IA. Discovery of 8-hydroxy-2-quinoline carbaldehyde derivatives as inhibitors for M1 aminopeptidase of Leishmania donovani. Int J Biol Macromol 2024; 279:135105. [PMID: 39197615 DOI: 10.1016/j.ijbiomac.2024.135105] [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: 04/30/2024] [Revised: 08/08/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
M1 aminopeptidase is a metallopeptidase that plays a vital role in protein catabolism and has been identified as a validated drug target in various parasites; however, our understanding of this enzyme is restricted for leishmanial parasite. The present investigation involved the purification of Leishmania donovani M1 aminopeptidase (LdM1AP) to homogeneity by affinity chromatography. Purified LdM1AP was observed to be enzymatically active and displayed maximal activity in the presence of cobalt ions, whereas secondary structure analysis confirmed the dominance of α-helices. Intrinsic fluorescence and quenching studies of LdM1AP has revealed that tryptophan residues were predominantly concealed within the hydrophobic areas. The synthesized 8-hydroxy-2-quinoline carbaldehyde derivatives were screened, wherein HQ2 and HQ12 were found as potent inhibitors for LdM1AP that compete with the substrate and exhibit pharmacokinetic properties as well as no toxicity for macrophages. Moreover, structural insights of protein and ligand complexes demonstrated that lead compounds mostly interact via hydrophobic contacts into the substrate binding pocket of LdM1AP. Furthermore, lead compounds exhibited a greater affinity for LdM1AP compared to the substrate during in vitro and in silico studies. This report establishes the possibility of quinoline derivatives to target the LdM1AP activity and provide a platform to design the specific antileishmanial drugs.
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Affiliation(s)
- Janish Kumar
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Jyotisha
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Rahila Qureshi
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Peddapaka Jagruthi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India
| | - Mohammed Arifuddin
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India.
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2
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Feng C, Wei H, Li X, Feng B, Xu C, Zhu X, Liu R. A stacking-based algorithm for antifreeze protein identification using combined physicochemical, pseudo amino acid composition, and reduction property features. Comput Biol Med 2024; 176:108534. [PMID: 38754217 DOI: 10.1016/j.compbiomed.2024.108534] [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: 02/04/2024] [Revised: 04/03/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024]
Abstract
Antifreeze proteins have wide applications in the medical and food industries. In this study, we propose a stacking-based classifier that can effectively identify antifreeze proteins. Initially, feature extraction was performed in three aspects: reduction properties, scalable pseudo amino acid composition, and physicochemical properties. A hybrid feature set comprised of the combined information from these three categories was obtained. Subsequently, we trained the training set based on LightGBM, XGBoost, and RandomForest algorithms, and the training outcomes were passed to the Logistic algorithm for matching, thereby establishing a stacking algorithm. The proposed algorithm was tested on the test set and an independent validation set. Experimental data indicates that the algorithm achieved a recognition accuracy of 98.3 %, and an accuracy of 98.5 % on the validation set. Lastly, we analyzed the reasons why numerical features achieved high recognition capabilities from multiple aspects. Data dimensionality reduction and the analysis from two-dimensional and three-dimensional views revealed separability between positive and negative samples, and the protein three-dimensional structure further demonstrated significant differences in related features between the two samples. Analysis of the classifier revealed that Hr*Hr, HrHr, and Sc-PseAAC_1, 188D(152,116,57,183) were among the seven most important numerical features affecting algorithm recognition. For Hr*Hr and HrHr, supportive sequence level evidence for the reduction dictionary was found in terms of conservation area analysis, multiple sequence alignment, and amino acid conservative substitution. Moreover, the importance of the reduction dictionary was recognized through a comparative analysis of importance before and after the reduction, realizing the effectiveness of the dictionary in improving feature importance. A decision tree model has been utilized to discern the distinctions between dipeptides associated with the physical and chemical properties of His(H), Iso(I), Leu(L), and Lys(K) and other dipeptides. We finally analyzed the other seven features of importance, and data analysis confirmed that hydrophobicity, secondary structure, charge properties, van der Waals forces, and solvent accessibility are also factors affecting the antifreeze capability of proteins.
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Affiliation(s)
- Changli Feng
- Department of Information Science and Technology, Taishan University, Taian, 271000, China.
| | - Haiyan Wei
- Department of Information Science and Technology, Taishan University, Taian, 271000, China.
| | - Xin Li
- Department of Information Science and Technology, Taishan University, Taian, 271000, China.
| | - Bin Feng
- Department of Information Science and Technology, Taishan University, Taian, 271000, China.
| | - Chugui Xu
- Department of Information Science and Technology, Taishan University, Taian, 271000, China.
| | - Xiaorong Zhu
- Department of Information Science and Technology, Taishan University, Taian, 271000, China.
| | - Ruijun Liu
- School of Software, Beihang University, Beijing, 100191, China.
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3
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Diessner EM, Takahashi GR, Martin RW, Butts CT. Comparative Modeling and Analysis of Extremophilic D-Ala-D-Ala Carboxypeptidases. Biomolecules 2023; 13:328. [PMID: 36830697 PMCID: PMC9953012 DOI: 10.3390/biom13020328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/21/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Understanding the molecular adaptations of organisms to extreme environments requires a comparative analysis of protein structure, function, and dynamics across species found in different environmental conditions. Computational studies can be particularly useful in this pursuit, allowing exploratory studies of large numbers of proteins under different thermal and chemical conditions that would be infeasible to carry out experimentally. Here, we perform such a study of the MEROPS family S11, S12, and S13 proteases from psychophilic, mesophilic, and thermophilic bacteria. Using a combination of protein structure prediction, atomistic molecular dynamics, and trajectory analysis, we examine both conserved features and trends across thermal groups. Our findings suggest a number of hypotheses for experimental investigation.
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Affiliation(s)
| | - Gemma R. Takahashi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Carter T. Butts
- Departments of Sociology, Statistics, Electrical Engineering and Computer Science, University of California, Irvine, CA 92697, USA
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4
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Piszkin L, Bowman J. Extremophile enzyme optimization for low temperature and high salinity are fundamentally incompatible. Extremophiles 2021; 26:5. [PMID: 34940913 DOI: 10.1007/s00792-021-01254-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022]
Abstract
The evolutionary mechanisms behind cold and high-saline co-adaptation of proteins are not thoroughly understood. To explore how enzymes evolve in response to multiple environmental pressures we developed a novel in silico method to model the directed evolution of proteins, the Protein Evolution Parameter Calculator (PEPC). PEPC carries out single amino acid substitutions that lead to improvements in the selected user-defined parameters. To investigate the evolutionary relationship between increased flexibility and decreased isoelectric point, which are presumed indicators of cold and saline adaptation in proteins, we applied PEPC to a subset of core haloarchaea orthologous group (cHOG) proteins from the mesophilic Halobacterium salinarum NRC-1 and cold-tolerant Halorubrum lacusprofundi strain ATCC 49239. The results suggest that mutations that increase flexibility will also generally increase isoelectric point. These findings suggest that enzyme adaptation to low temperature and high salinity might be evolutionarily counterposed based on the structural characteristics of probable amino acid mutations. This may help to explain the apparent lack of truly psychrophilic halophiles in nature, and why microbes adapted to polar hypersaline environments typically have mesophilic temperature optima. A better understanding of protein evolution to extremely cold and salty conditions will aid in our understanding of where and how life is distributed on Earth and in our solar system.
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Affiliation(s)
- Luke Piszkin
- Department of Physics, UC San Diego, La Jolla, CA, USA.
| | - Jeff Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
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5
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Pang WC, Ramli ANM, Hamid AAA. Comparative modelling studies of fruit bromelain using molecular dynamics simulation. J Mol Model 2020; 26:142. [PMID: 32417971 DOI: 10.1007/s00894-020-04398-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/28/2020] [Indexed: 12/25/2022]
Abstract
Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.
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Affiliation(s)
- Wei Cheng Pang
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Aizi Nor Mazila Ramli
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia. .,Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
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6
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Thakur N, Sharma N, Kumar V, Bhalla TC. Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190718150627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Amidases are ubiquitous enzymes and biological functions of these enzymes
vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of
carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals
synthesis, pharmaceuticals agrochemicals and wastewater treatments.
Methods:
They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides,
arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic
site and preferred substrate. Despite their economic importance, we lack knowledge as to how these
amidases withstand elevated pH and temperature whereas others cannot.
Results:
The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant
and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic
organisms revealed some striking trends as to how amino acid composition varies significantly.
Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of
these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L)
in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant
and alkali tolerant amidases.
Conclusion:
The present investigation insights physiochemical properties and dominance of some crucial
amino acid residues in the primary and secondary structure of some amidases from acid-tolerant,
alkali tolerant and neutrophilic microorganisms.
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Affiliation(s)
- Neerja Thakur
- Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Nikhil Sharma
- Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Vijay Kumar
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
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7
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Bhat SY, Qureshi IA. Mutations of key substrate binding residues of leishmanial peptidase T alter its functional and structural dynamics. Biochim Biophys Acta Gen Subj 2020; 1864:129465. [DOI: 10.1016/j.bbagen.2019.129465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/15/2019] [Accepted: 10/24/2019] [Indexed: 11/27/2022]
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Structural features of cold-adapted dimeric GH2 β-D-galactosidase from Arthrobacter sp. 32cB. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:776-786. [PMID: 31195142 DOI: 10.1016/j.bbapap.2019.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 05/12/2019] [Accepted: 06/06/2019] [Indexed: 12/21/2022]
Abstract
Crystal structures of cold-adapted β-d-galactosidase (EC 3.2.1.23) from the Antarctic bacterium Arthrobacter sp. 32cB (ArthβDG) have been determined in an unliganded form resulting from diffraction experiments conducted at 100 K (at resolution 1.8 Å) and at room temperature (at resolution 3.0 Å). A detailed comparison of those two structures of the same enzyme was performed in order to estimate differences in their molecular flexibility and rigidity and to study structural rationalization for the cold-adaptation of the investigated enzyme. Furthermore, a comparative analysis with structures of homologous enzymes from psychrophilic, mesophilic, and thermophilic sources has been discussed to elucidate the relationship between structure and cold-adaptation in a wider context. The performed studies confirm that the structure of cold-adapted ArthβDG maintains balance between molecular stability and structural flexibility, which can be observed independently on the temperature of conducted X-ray diffraction experiments. Obtained information about proper protein function under given conditions provide a guideline for rational engineering of proteins in terms of their temperature optimum and thermal stability.
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9
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Devi S, Savitri, Raj T, Sharma N, Azmi W. In silicoAnalysis of L-Glutaminase from Extremophiles. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164615666180911110606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:L-glutaminase enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amides. Protein L-glutaminase, which converts amino acid glutamine to a glutamate residue, is useful as antileukemic agent, antiretroviral agent and a new food-processing enzyme.Objective:The sequences representing L-glutaminase from extremophiles were analyzed for different physico-chemical properties and to relate these observed differences to their extremophilic properties, phylogenetic tree construction and the evolutionary relationship among them.Methods:In this work, in silico analysis of amino acid sequences of extremophilic (thermophile, halophile and psychrophiles) proteins has been done. The physiochemical properties of these four groups of proteins for L-glutaminase also differ in number of amino acids, aliphatic index and grand average of hydropathicity (GRAVY).Result:The GRAVY was found to be significantly high in thermophilic (2.29 fold) and psychrophilic bacteria (3.3 fold) as compare to mesophilic bacteria. The amino acid Cys (C) was found to be statistically significant in mesophilic bacteria (approximately or more than 3 fold) as compared to the abundance of this amino acid in extremophilic bacteria.Conclusion:Multiple sequence alignment revealed the domain/motif for glutaminase that consists of Ser-74, Lys-77, Asn-126, Lys-268, and Ser-269, which is highly conserved in all microorganisms.
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Affiliation(s)
- Sarita Devi
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, India
| | - Savitri
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, India
| | - Tilak Raj
- Sub-Distributed Information Centre, Himachal Pradesh University, Summer Hill, Shimla, India
| | - Nikhil Sharma
- Sub-Distributed Information Centre, Himachal Pradesh University, Summer Hill, Shimla, India
| | - Wamik Azmi
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, India
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10
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Ng ML, Rahmat ZB, Bin Omar MSS. Molecular Modeling and Simulation of Transketolase from Orthosiphon stamineus. Curr Comput Aided Drug Des 2018; 15:308-317. [PMID: 30345923 DOI: 10.2174/1573409914666181022141753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/21/2018] [Accepted: 10/17/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Orthosiphon stamineus is a traditional medicinal plant in Southeast Asia countries with various well-known pharmacological activities such as antidiabetic, diuretics and antitumor activities. Transketolase is one of the proteins identified in the leaves of the plant and transketolase is believed able to lower blood sugar level in human through non-pancreatic mechanism. In order to understand the protein behavioral properties, 3D model of transketolase and analysis of protein structure are of obvious interest. METHODS In the present study, 3D model of transketolase was constructed and its atomic characteristics revealed. Besides, molecular dynamic simulation of the protein at 310 K and 368 K deciphered transketolase may be a thermophilic protein as the structure does not distort even at elevated temperature. This study also used the protein at 310 K and 368 K resimulated back at 310 K environment. RESULTS The results revealed that the protein is stable at all condition which suggest that it has high capacity to adapt at different environment not only at high temperature but also from high temperature condition to low temperature where the structure remains unchanged while retaining protein function. CONCLUSION The thermostability properties of transketolase is beneficial for pharmaceutical industries as most of the drug making processes are at high temperature condition.
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Affiliation(s)
- Mei Ling Ng
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 (Skudai), Johor, Malaysia
| | - Zaidah Binti Rahmat
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 (Skudai), Johor, Malaysia
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11
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Brininger C, Spradlin S, Cobani L, Evilia C. The more adaptive to change, the more likely you are to survive: Protein adaptation in extremophiles. Semin Cell Dev Biol 2018; 84:158-169. [PMID: 29288800 DOI: 10.1016/j.semcdb.2017.12.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/25/2017] [Accepted: 12/25/2017] [Indexed: 12/22/2022]
Abstract
Discovering how organisms and their proteins adapt to extreme conditions is a complicated process. Every condition has its own set of adaptations that make it uniquely stable in its environment. The purpose of our review is to discuss what is known in the extremophilic community about protein adaptations. To simplify our mission, we broke the extremophiles into three broad categories: thermophiles, halophiles and psychrophiles. While there are crossover organisms- organisms that exist in two or more extremes, like heat plus acid or cold plus pressure, most of them have a primary adaptation that is within one of these categories which tends to be the most easily identifiable one. While the generally known adaptations are still accepted, like thermophilic proteins have increased ionic interactions and a hardier hydrophobic core, halophilic proteins have a large increase in acidic amino acids and amino acid/peptide insertions and psychrophiles have a much more open structure and reduced ionic interactions, some new information has come to light. Thermophilic stability can be improved by increased subunit-subunit or subunit-cofactor interactions. Halophilic proteins have reversible folding when in the presence of salt. Psychrophilic proteins have an increase in cavities that not only decrease the formation of ice, but also increase flexibility under low temperature conditions. In a proof of concept experiment, we applied what is currently known about adaptations to a well characterized protein, malate dehydrogenase (MDH). While this protein has been profiled in the literature, we are applying our adaptation predictions to its sequence and structure to see if the described adaptations apply. Our analysis demonstrates that thermophilic and halophilic adaptations fit the corresponding MDHs very well. However, because the number of psychrophiles MDH sequences and structures is low, our analysis on psychrophiles is inconclusive and needs more information. By discussing known extremophilic adaptations and applying them to a random, conserved protein, we have found that general adaptations are conserved and can be predicted in proposed extremophilic proteins. The present field of extremophile adaptations is discovering more and more ways organisms and their proteins have adapted. The more that is learned about protein adaptation, the closer we get to custom proteins, designed to fit any extreme and solve some of the world's most pressing environmental problems.
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Affiliation(s)
- C Brininger
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - S Spradlin
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - L Cobani
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - C Evilia
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA.
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12
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Sabljić I, Tomin M, Matovina M, Sučec I, Tomašić Paić A, Tomić A, Abramić M, Tomić S. The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity. PLoS One 2018; 13:e0192488. [PMID: 29420664 PMCID: PMC5805324 DOI: 10.1371/journal.pone.0192488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/24/2018] [Indexed: 12/14/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) isolated from the thermophilic bacteria Caldithrix abyssi (Ca) is a two-domain zinc exopeptidase, a member of the M49 family. Like other DPPs III, it cleaves dipeptides from the N-terminus of its substrates but differently from human, yeast and Bacteroides thetaiotaomicron (mesophile) orthologs, it has the pentapeptide zinc binding motif (HEISH) in the active site instead of the hexapeptide (HEXXGH). The aim of our study was to investigate structure, dynamics and activity of CaDPP III, as well as to find possible differences with already characterized DPPs III from mesophiles, especially B. thetaiotaomicron. The enzyme structure was determined by X-ray diffraction, while stability and flexibility were investigated using MD simulations. Using molecular modeling approach we determined the way of ligands binding into the enzyme active site and identified the possible reasons for the decreased substrate specificity compared to other DPPs III. The obtained results gave us possible explanation for higher stability, as well as higher temperature optimum of CaDPP III. The structural features explaining its altered substrate specificity are also given. The possible structural and catalytic significance of the HEISH motive, unique to CaDPP III, was studied computationally, comparing the results of long MD simulations of the wild type enzyme with those obtained for the HEISGH mutant. This study presents the first structural and biochemical characterization of DPP III from a thermophile.
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Affiliation(s)
- Igor Sabljić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marko Tomin
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Mihaela Matovina
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Iva Sučec
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antonija Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail:
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Panja AS, Bandopadhyay B, Maiti S. Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges. PLoS One 2015; 10:e0131495. [PMID: 26177372 PMCID: PMC4503463 DOI: 10.1371/journal.pone.0131495] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/01/2015] [Indexed: 01/08/2023] Open
Abstract
Introduction Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications. Methods Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins. Results Present results strongly suggest that nonpolar smaller volume amino acids Ala (χ2 = 238.54, p<0.001) and Gly (χ2 = 73.35, p<0.001) are highly and Val moderately (χ2 = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (χ2~20.0, p<0.01) in a larger number of thermophilic proteins. A consistent lower distribution of thermophilicity and discretely higher distribution of hydrophobicity is noticed in a large number of thermophilic versus their mesophilic protein homolog. The mean differences of isoelectric points and charges are found to be significantly less (7.11 vs. 6.39, p<0.05 and 1 vs. -0.6, p<0.01, respectively) in thermophilic proteins compared to their mesophilic counterpart. The possible sites for Tyr phosphorylation are noticed to be 25% higher (p<0.05) in thermophilic proteins. The 60% thermophiles are found with higher number of salt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (p<0.05 and p<0.001, respectively) in thermophilic and GLU-ARG is higher in the mesophilic proteins. The Ramachandran plot/ data suggest a higher abundance of the helix, left-handed helix, sheet, nonplanar peptide and lower occurrence of cis peptide, loop/ turn and outlier in thermophiles. Pearson’s correlation result suggests that the isoelectric points of mesophilic and thermophilic proteins are positively correlated (r = 0.93 and 0.84, respectively; p<0.001) to their corresponding charges. And their hydrophilicity is negatively associated with the corresponding hydrophobicity (r = -0.493, p<0.001 and r = -0.324, p<0.05) suggesting their reciprocal evolvement. Conclusions Present results for the first time with this large amount of datasets and multiple contributing factors suggest the greater occurrence of hydrophobicity, salt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins.
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Affiliation(s)
- Anindya Sundar Panja
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India
| | - Bidyut Bandopadhyay
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India
| | - Smarajit Maiti
- Post Graduate Department of Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, 721102, West Bengal, India
- * E-mail:
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