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Characterization and 3d structure prediction of chitinase induced in sugarcane during pathogenesis of Colletotrichum falcatum

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JOURNAL OF PLANT BIOCHEMISTRY ANd BIOTECHNOLOGY 2015年第1期24卷 1-8页

作者： Rahul, P. R. Kumar, V. Ganesh Sathyabhama, M. Viswanathan, R. Sundar, A. Ramesh Malathi, P. Indian Council Agr Res Sugarcane Breeding Inst Div Crop Protect Plant Pathol Sect Coimbatore 641007 Tamil Nadu India Indian Council Agr Res Sugarcane Breeding Inst Div Crop Protect Coimbatore 641007 Tamil Nadu India

Chitinases are known to play an important role in many host-pathogen interactions. To reveal the defense associated role of chitinases in sugarcane during interaction with Colletotrichum falcatum causing red rot, detailed studies were conducted on the expression of chitinases in sugarcane cultivars varying in disease resistance, their characterization and theoretical 3d structure prediction through transcriptomic and bioinformatics tools. Partial mRNA sequences of chitinase corresponding to 782 bp were amplified from red rot resistant (Co 93009) and susceptible (CoC 671) cultivars. The relative expression of chitinase gene in both the cultivars by qRT-PCR showed a high level of expression only in the resistant cultivar. Consequently, the full length chitinase sequence ScChiB1 corresponding to 840 bp fragment was isolated from the red rot resistant cv Co 93009. Translated amino acid sequence of the full length sugarcane chitinase gene ScChiB1 from sugarcane cv Co 93009 revealed the typical characteristics of classes I/IV chitinase starting with a signal peptide and ending with a signature domain. Phylogenetic analysis grouped ScChiB1 in class IV, based upon major deletions in catalytic domain. Protein structure modeling (3d) using rice class I chitinase (2dKV) as a template also clearly revealed structural differences due to the presence of three deletions in the catalytic domains of sugarcane class IV chitinase. This concluded that the predicted structure of sugarcane chitinase ScChiB1 belongs to class IV of family 19 glycosyl hydrolases.

关键词： Sugarcane chitinase Red rot Colletotrichum falcatum qRT-PCR 3d structure prediction Class IV chitinase Signal peptide Secretory pathway bi-lobed chitin binding domain

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Using 3dRNA/dNA for RNA and dNA 3d structure prediction and Evaluation

CURRENT PROTOCOLS

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CURRENT PROTOCOLS 2023年第5期3卷 e770页

作者： Xiong, Yiduo Zhang, Yi Wang, Jian Xiao, Yi Huazhong Univ Sci & Technol Inst Biophys Sch Phys Wuhan Hubei Peoples R China

This article describes how to use 3dRNA/dNA to predict RNA and dNA 3d structures from their sequences and secondary (2d) structures. The predicted RNA and dNA 3d structures can be used to predict or understand their functions and can also be used to find the interactions between the RNA/dNA and other molecules. (c) 2023 Wiley Periodicals LLC. Basic Protocol: RNA/dNA 3d structure prediction using 3dRNA/dNA web server Alternate Protocol: Using 3dRNA/dNA and 3dRNAscore locally Support Protocol: Installing NSP

关键词： 3dRNA/dNA 3d structure prediction circular RNA dNA linear RNA

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An Integrated Tool for RNA 3d structure prediction and Analysis 33

An Integrated Tool for RNA 3D Structure Prediction and Analy...

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33rd Chinese Control and decision Conference (CCdC)

作者： Yuan, Li Guo, Zhi-Hao Cao, Wen-Jie Luo, Yong Shi, Ya-Zhou Wuhan Text Univ Res Ctr Nonlinear Sci Sch Math & Comp Sci Wuhan 430200 Peoples R China Guangdong Yixun Technol Co Ltd Publ R&D Ctr Architecture Lab Wuhan 430073 Peoples R China

ISBN: (纸本)9781665440899

Since the knowledge of the 3d structures of RNAs is a fundamental prerequisite to completely understand the functions of RNAs. In this work, we have integrated the existing RNA 3d structure prediction models and structural analysis methods (e.g., the dSSR software and the script of ***) into a new tool to realize the 3d structure prediction and analysis for RNAs with sequences and secondary structures as input. Although only the models with ready-made web server are integrated in the present version of the tool, our test on 3d structures prediction for different RNAs indicates that integrating the existing models is very necessary to accurately predict RNA 3d structures.

关键词： RNA 3d structure prediction Integration Structural Analysis

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An Integrated Tool for RNA 3d structure prediction and Analysis

An Integrated Tool for RNA 3D Structure Prediction and Analy...

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第33届中国控制与决策会议

作者： Li Yuan Zhi-Hao Guo Wen-Jie Cao Yong Luo Ya-Zhou Shi Research Center of Nonlinear Science School of Mathematics and Computer ScienceWuhan Textile University Public R&D Center Architecture Laboratory Guangdong Yixun Technology Company Limited

Since the knowledge of the 3d structures of RNAs is a fundamental prerequisite to completely understand the functions of *** this work,we have integrated the existing RNA 3d structure prediction models and structural analysis methods（e.g.,the dSSR software and the script of rmsd·PyPI） into a new tool to realize the 3d structure prediction and analysis for RNAs with sequences and secondary structures as *** only the models with ready-made web server are integrated in the present version of the tool,our test on 3d structures prediction for different RNAs indicates that integrating the existing models is very necessary to accurately predict RNA 3d structures.

关键词： RNA 3d structure prediction Integration Structural Analysis

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Fusion of two unrelated protein domains in a chimera protein and its 3d prediction: Justification of the x-ray reference structures as a prediction benchmark

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PROTEINS-structure FUNCTION ANd BIOINFORMATICS 2022年第12期90卷 2067-2079页

作者： Vymetal, Jiri Mertova, Katerina Bousova, Kristyna Sulc, Josef Tripsianes, Konstantinos Vondrasek, Jiri Czech Acad Sci Inst Organ Chem & Biochem Flemingovo Namesti 2 Prague 16000 6 Czech Republic Charles Univ Prague Fac Nat Sci Prague 2 Czech Republic Masaryk Univ Cent European Inst Technol Brno Czech Republic

Proteins are naturally formed by domains edging their functional and structural properties. A domain out of the context of an entire protein can retain its structure and to some extent also function on its own. These properties rationalize construction of artificial fusion multidomain proteins with unique combination of various functions. Information on the specific functional and structural characteristics of individual domains in the context of new artificial fusion proteins is inevitably encoded in sequential order of composing domains defining their mutual spatial positions. So the challenges in designing new proteins with new domain combinations lie dominantly in structure/function prediction and its context dependency. despite the enormous body of publications on artificial fusion proteins, the task of their structure/function prediction is complex and nontrivial. The degree of spatial freedom facilitated by a linker between domains and their mutual orientation driven by noncovalent interactions is beyond a simple and straightforward methodology to predict their structure with reasonable accuracy. In the presented manuscript, we tested methodology using available modeling tools and computational methods. We show that the process and methodology of such prediction are not straightforward and must be done with care even when recently introduced AlphaFold II is used. We also addressed a question of benchmarking standards for prediction of multidomain protein structures-x-ray or Nuclear Magnetic Resonance experiments. On the study of six two-domain protein chimeras as well as their composing domains and their x-ray structures selected from PdB, we conclude that the major obstacle for justified prediction is inappropriate sampling of the conformational space by the explored methods. On the other hands, we can still address particular steps of the methodology and improve the process of chimera proteins prediction.

关键词： 3d structure prediction fusion proteins molecular simulations x-ray crystallography

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In silico designing of therapeutic protein enriched with branched-chain amino acids for the dietary treatment of chronic liver disease

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JOURNAL OF MOLECULAR GRAPHICS & MOdELLING 2017年 76卷 192-204页

作者： Sunil, L. Vasu, Prasanna CSIR Cent Food Technol Res Inst Dept Food Safety Mysuru 570020 Karnataka India CSIR Cent Food Technol Res Inst Analyt Qual Control Lab Mysuru 570020 Karnataka India

Leucine, isoleucine, and valine are three essential branched-chain amino acids (BCAA) account for 40-45% of total essential amino acids. BCAA stimulates protein synthesis primarily in skeletal muscles, and it can directly transport to circulatory blood stream bypassing the liver. Hence, a protein enriched with BCAA is an important therapeutic target for the dietary treatment of chronic liver disease. The present study is to design a synthetic protein enriched with BCAA and the challenge is to maximize the BCAA content, keeping the balanced ratio of leucine, isoleucine, valine - 2: 1: 1.2 as specified by WHO/UNU/FAO. Here, we turned the general concept of homology modeling and tried to find a suitable scaffold (alpha-helix) to host an excess amount of BCAA for increased stability and digestibility. A total of 50 protein models were constructed by using SWISS-MOdEL, Modeller 9.17, ProtParam tool, and allergen online tools. Out of 50 different protein models, protein model-50 was found to be best, which had a well-defined 3d structure, good in silico digestibility, balanced ratio of BCAA and showed 65.57% structure identity to the template apo-bovine alpha-lactalbumin (1F6R). Templates search was performed against PdB using PSI-BLAST, SWISS MOdEL, PROFUNC, I-TASSER, and ConSurf. The secondary structure was predicted by PSSPred, PSIPREd, I-TASSER, PORTER, and SPIdER2. The modeled structure of protein Model-50 was validated by PROCHECK, ERRAT, ProSA, and QMEAN. COACH and ProFUNC tools were performed to determine the functional effects of protein model-50. Overall, the BCAA was enriched from 22 to 56.4% with the balanced ratio of Leu: Ile: Val (2: 1: 1.2). The Ramachandran plot showed 97.7% of the amino acid residues in allowed regions with ERRAT score of 86.05. We have successfully modeled the complete three-dimensional structure of the target protein model-50 using highly reputed computational tools. (C) 2017 Elsevier Inc. All rights reserved.

关键词： Branched-chain amino acids (BCAA) Homology modeling Apo-bovine alpha-lactalbumin Secondary structure prediction 3d structure prediction Protein validation

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Cloning, sequence analysis and three-dimensional structure prediction of dNA pol I from thermophilic Geobacillus sp MKK isolated from an Iranian hot spring

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APPLIEd BIOCHEMISTRY ANd BIOTECHNOLOGY 2007年第2期142卷 200-208页

作者： Khalaj-Kondori, Mohammad Sadeghizadeh, Majid Khajeh, Khosro Naderi-Manesh, Hossein Ahadi, Ali Mohammad Emamzadeh, Abdorahman Tarbiat Modares Univ Fac Basic Sci Dept Biol Tehran 14115 Iran

Molecular phylogenetic analysis of a novel thermophilic eubacterium isolated from an Iranian hot spring using 16S rdNA sequence showed that the new isolate belongs to genera Geobacillus. dNA pol I gene from this isolate was amplified, cloned, sequenced, and the three-dimensional (3d) structure of deduced amino acid sequence was predicted. Sequence analysis revealed the gene is 2,631 bp long, encodes a protein of 876 amino acids with a calculated molecular mass of 99 kda, and belongs to family A dNA polymerases. Comparison of 3'-5'exonuclease domain of Klenow fragment (KF) with corresponding region of newly identified dNA pol I (MF), the large fragment of Bacillus stearothermophilus dNA pol I (BF) and Klentaq1, revealed not only deletions in three regions compared to KF, but that three of the four critical metal-binding residues in KF (Asp355, Glu357, Asp424, and Asp501) are altered in MF as well. Predicted 3d structure and sequence alignments between MF and BF showed that all critical residues in the polymerase active site are conserved.

关键词： molecular phylogenetic thermostable dNA pol I cloning 3d structure prediction gsm pol I

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Bioinformatics: A Molecular Microbiologist's Perspective

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CURRENT BIOINFORMATICS 2014年第1期9卷 8-17页

作者： Sousa, Silvia A. Feliciano, Joana R. Grilo, Andre M. Leitao, Jorge H. Univ Lisbon Inst Super Tecn Dept Bioengn Ctr Biol & Chem EngnIBB Inst Biotechnol & Bioeng P-1049001 Lisbon Portugal Univ Lisbon Inst Super Tecn Dept Bioengn P-1049001 Lisbon Portugal Univ Lisbon Inst Super Tecn Ctr Biol & Chem Engn P-1049001 Lisbon Portugal

Research activities in the area of biological sciences, and particularly molecular microbiology, nowadays generate vast amounts of data. The development of faster and cheaper sequencing methods has definitively contributed to this huge amount of data, requiring the development of fast and reliable tools for their analysis. In the last years, many easy-to-use, reliable and powerful bioinformatics tools have been developed. In this work, we review the fundamentals of some of these tools, and describe how we have been using them to analyze data resulting from our research envisaging the identification and characterization of virulence factors and determinants from the human opportunistic pathogens of the Burkholderia cepacia complex. Examples given illustrate the user-friendly characteristic of these tools and their power both in analyzing information and in orientating future experimental work.

关键词： Bacterial virulence factor identification bioinformatics tools 3d structure prediction protein function prediction protein interaction prediction sequence alignments

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Flat or angular? The impact of the nitrogen atom hybridization on the docking results for arylpiperazine derivatives as an example

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STRUCTURAL CHEMISTRY 2020年第2期31卷 823-829页

作者： Rzesikowska, Katarzyna Jablonski, Mateusz Kalinowska-Tluscik, Justyna Jagiellonian Univ Dept Crystal Chem & Crystal Phys Fac Chem Gronostajowa 2 PL-30387 Krakow Poland

structure-based virtual screening has become a standard approach in modern drug discovery. It involves molecular docking and estimation of the ligand binding likelihood based on the scoring function. Surprisingly, in the search for new pharmaceuticals, one of the bottlenecks can be the ligand's 3d structure prediction, especially for molecules with amine groups. In our work, the impact of the nitrogen atom hybridization in arylpiperazine derivatives on the results of docking to serotonin receptor type 7 is discussed. Our docking/re-docking studies show that the nitrogen lone pair may be involved in weak ligand-protein interactions. The presented results suggest that assumption of amine group planarity in the arylpiperazine 3d structure prediction may be a misleading factor in computer-aided drug discovery, influencing active conformation prediction. With our paper, we would like to raise awareness that in the case of compounds with amine groups, special care must be taken in the 3d ligand's structure preparation for molecular docking studies.

关键词： Arylpiperazine derivatives 3d structure prediction Virtual screening

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Comparative structural analysis of fruit and stem bromelain from Ananas comosus

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FOOd CHEMISTRY 2018年 266卷 183-191页

作者： Ramli, Aizi Nor Mazila Manas, Nor Hasmaliana Abdul Hamid, Azzmer Azzar Abdul Abd Hamid, Hazrulrizawati Illias, Rosli Md. Univ Malaysia Pahang Fac Ind Sci & Technol Kuantan 26300 Pahang Darul Ma Malaysia Univ Teknol Malaysia Fac Chem & Energy Engn Dept Bioproc & Polymer Engn Skudai 81310 Johor Malaysia Int Islamic Univ Malaysia Kulliyyah Sci Dept Biotechnol Jalan Sultan Ahmad Shah Kuantan 25200 Pahang Malaysia

Cysteine proteases in pineapple (Ananas comosus) plants are phytotherapeutical agents that demonstrate antiedematous, anti-inflammatory, anti-thrombotic and fibrinolytic activities. Bromelain has been identified as an active component and as a major protease of A. comosus. Bromelain has gained wide acceptance and compliance as a phytotherapeutical drug. The proteolytic fraction of pineapple stem is termed stem bromelain, while the one presents in the fruit is known as fruit bromelain. The amino acid sequence and domain analysis of the fruit and stem bromelains demonstrated several differences and similarities of these cysteine protease family members. In addition, analysis of the modelled fruit (BAA21848) and stem (CAA08861) bromelains revealed the presence of unique properties of the predicted structures. Sequence analysis and structural prediction of stem and fruit bromelains of A. comosus along with the comparison of both structures provides a new insight on their distinct properties for industrial application.

关键词： Stem bromelain Fruit bromelain Amino acid analysis 3d structure prediction

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