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Damtie D, Gelaw A, Wondimeneh Y, Aleka Y, Kick MK, Tigabu Z, Sack U, Mekuria ZH, Vlasova AN, Tessema B. Rotavirus A Infection Prevalence and Spatio-Temporal Genotype Shift among Under-Five Children in Amhara National Regional State, Ethiopia: A Multi-Center Cross-Sectional Study. Vaccines (Basel) 2024; 12:866. [PMID: 39203992 PMCID: PMC11360187 DOI: 10.3390/vaccines12080866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 07/24/2024] [Accepted: 07/28/2024] [Indexed: 09/03/2024] Open
Abstract
Background: Globally, rotavirus (RV) A (RVA) is the most common cause of severe and sometimes fatal diarrhea in young children. It is also the major cause of acute gastroenteritis among children in Ethiopia. Currently, the WHO has prequalified four RVA vaccines for universal childhood immunization. Ethiopia introduced the monovalent Rotarix vaccine into its national immunization program in 2013. Since then, only a few studies on the burden and genotype distribution of RVA infection post-vaccine introduction have been conducted (mostly at sentinel surveillance sites). Therefore, this study aimed to assess RVA prevalence and genotype distribution among children under five years in Ethiopia (February 2021-December 2022). Methods: This multi-center hospital-based cross-sectional study involved 537 diarrheic children under-five years old. Rotavirus A detection was conducted using a one-step reverse-transcriptase polymerase chain reaction (RT-PCR). Genotyping was conducted by Sanger sequencing of the VP7 (complete) and VP4 (partial) genes. Descriptive analysis and Pearson's chi-squared test were carried out using SPSS version 29. Phylogenetic analysis with 1000 bootstrap replicates was performed using MEGA version 11 software. Statistical significance was set at p < 0.05 for all analyses. Results: The prevalence of RVA infection among diarrheic children was 17.5%. The most prevalent G-types identified were G3 (37%), the previously uncommon G12 (28%), and G1 (20%). The predominant P-types were P[8] (51%), P[6] (29%), and P[4] (14%). The three major G/P combinations observed were G3P[8] (32.8%), G12P[6] (28.4%), and G1P[8] (19.4%). Phylogenetic analysis revealed clustering of Ethiopian strains with the globally reported strains. Many strains exhibited amino acid differences in the VP4 (VP8* domain) and VP7 proteins compared to vaccine strains, potentially affecting virus neutralization. Conclusions: Despite the high RVA vaccination rate, the prevalence of RVA infection remains significant among diarrheic children in Ethiopia. There is an observable shift in circulating RVA genotypes from G1 to G3, alongside the emergence of unusual G/P genotype combinations such as G9P[4]. Many of these circulating RVA strains have shown amino acid substitutions that may allow for neutralization escape. Therefore, further studies are warranted to comprehend the emergence of these unusual RVA strains and the diverse factors influencing the vaccine's diminished effectiveness in developing countries.
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Affiliation(s)
- Debasu Damtie
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia; (A.G.); (Y.W.); (B.T.)
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia;
- Ohio State University Global One Health Initiative LLC, Eastern Africa Regional Office, Bole Road, Noah Plaza, 2nd Floor, Addis Ababa, Ethiopia
- Center for Food Animal Health, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA;
| | - Aschalew Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia; (A.G.); (Y.W.); (B.T.)
| | - Yitayih Wondimeneh
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia; (A.G.); (Y.W.); (B.T.)
| | - Yetemwork Aleka
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia;
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
| | - Maryssa K. Kick
- Center for Food Animal Health, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA;
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Zemene Tigabu
- Department of Pediatrics and Child Health, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia;
| | - Ulrich Sack
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
| | - Zelalem H. Mekuria
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH 43210, USA
| | - Anastasia N. Vlasova
- Center for Food Animal Health, Department of Animal Sciences, College of Food Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA;
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Belay Tessema
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia; (A.G.); (Y.W.); (B.T.)
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
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2
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Kang JM, Park JS, Lee JS, Jang JY, Han BW. Structural study for substrate recognition of human N-terminal glutamine amidohydrolase 1 in the arginine N-degron pathway. Protein Sci 2024; 33:e5067. [PMID: 38864716 PMCID: PMC11168063 DOI: 10.1002/pro.5067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/12/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024]
Abstract
The N-degron pathway determines the half-life of proteins by selectively destabilizing the proteins bearing N-degrons. N-terminal glutamine amidohydrolase 1 (NTAQ1) plays an essential role in the arginine N-degron (Arg/N-degron) pathway as an initializing enzyme via the deamidation of the N-terminal (Nt) glutamine (Gln). However, the Nt-serine-bound conformation of hNTAQ1 according to the previously identified crystal structure suggests the possibility of other factors influencing the recognition of Nt residues by hNTAQ1. Hence, in the current study, we aimed to further elucidate the substrate recognition of hNTAQ1; specifically, we explored 12 different substrate-binding conformations of hNTAQ1 depending on the subsequent residue of Nt-Gln. Results revealed that hNTAQ1 primarily interacts with the protein Nt backbone, instead of the side chain, for substrate recognition. Here, we report that the Nt backbone of proteins appears to be a key component of hNTAQ1 function and is the main determinant of substrate recognition. Moreover, not all second residues from Nt-Gln, but rather distinctive and charged residues, appeared to aid in detecting substrate recognition. These new findings define the substrate-recognition process of hNTAQ1 and emphasize the importance of the subsequent Gln residue in the Nt-Gln degradation system. Our extensive structural and biochemical analyses provide insights into the substrate specificity of the N-degron pathway and shed light on the mechanism underlying hNTAQ1 substrate recognition. An improved understanding of the protein degradation machinery could aid in developing therapies to promote overall health through enhanced protein regulation, such as targeted protein therapies.
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Affiliation(s)
- Jin Mo Kang
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Jae Seok Lee
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Jun Young Jang
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
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3
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Prabhu H, Bhosale H, Sane A, Dhadwal R, Ramakrishnan V, Valadi J. Protein feature engineering framework for AMPylation site prediction. Sci Rep 2024; 14:8695. [PMID: 38622194 PMCID: PMC11369087 DOI: 10.1038/s41598-024-58450-8] [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: 11/13/2023] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
AMPylation is a biologically significant yet understudied post-translational modification where an adenosine monophosphate (AMP) group is added to Tyrosine and Threonine residues primarily. While recent work has illuminated the prevalence and functional impacts of AMPylation, experimental identification of AMPylation sites remains challenging. Computational prediction techniques provide a faster alternative approach. The predictive performance of machine learning models is highly dependent on the features used to represent the raw amino acid sequences. In this work, we introduce a novel feature extraction pipeline to encode the key properties relevant to AMPylation site prediction. We utilize a recently published dataset of curated AMPylation sites to develop our feature generation framework. We demonstrate the utility of our extracted features by training various machine learning classifiers, on various numerical representations of the raw sequences extracted with the help of our framework. Tenfold cross-validation is used to evaluate the model's capability to distinguish between AMPylated and non-AMPylated sites. The top-performing set of features extracted achieved MCC score of 0.58, Accuracy of 0.8, AUC-ROC of 0.85 and F1 score of 0.73. Further, we elucidate the behaviour of the model on the set of features consisting of monogram and bigram counts for various representations using SHapley Additive exPlanations.
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Affiliation(s)
- Hardik Prabhu
- Computing and Data Sciences, FLAME University, Pune, 412115, India
- Robert Bosch Centre for Cyber Physical Systems, Indian Institute of Science, Bengaluru, 560012, India
| | | | - Aamod Sane
- Computing and Data Sciences, FLAME University, Pune, 412115, India
| | - Renu Dhadwal
- Computing and Data Sciences, FLAME University, Pune, 412115, India
| | - Vigneshwar Ramakrishnan
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
| | - Jayaraman Valadi
- Computing and Data Sciences, FLAME University, Pune, 412115, India.
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4
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Chennakesavalu S, Rotskoff GM. Data-Efficient Generation of Protein Conformational Ensembles with Backbone-to-Side-Chain Transformers. J Phys Chem B 2024; 128:2114-2123. [PMID: 38394363 DOI: 10.1021/acs.jpcb.3c08195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike image generation or even the closely related problem of protein structure prediction, there are currently no data sources with sufficient breadth to parametrize generative models for conformational ensembles. To enable discovery, a fundamentally different approach to building generative models is required: models should be able to propose rare, albeit physical, conformations that may not arise in even the largest data sets. Here we introduce a modular strategy to generate conformations based on "backmapping" from a fixed protein backbone that (1) maintains conformational diversity of the side chains and (2) couples the side-chain fluctuations using global information about the protein conformation. Our model combines simple statistical models of side-chain conformations based on rotamer libraries with the now ubiquitous transformer architecture to sample with atomistic accuracy. Together, these ingredients provide a strategy for rapid data acquisition and hence a crucial ingredient for scalable physical simulation with generative neural networks.
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Affiliation(s)
| | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
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5
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Chen X, Kriebisch BAK, Bergmann AM, Boekhoven J. Design rules for reciprocal coupling in chemically fueled assembly. Chem Sci 2023; 14:10176-10183. [PMID: 37772095 PMCID: PMC10530897 DOI: 10.1039/d3sc02062b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
Biology regulates the function and assembly of proteins through non-equilibrium reaction cycles. Reciprocally, the assembly of proteins can influence the reaction rates of these cycles. Such reciprocal coupling between assembly and reaction cycle is a prerequisite for behavior like dynamic instabilities, treadmilling, pattern formation, and oscillations between morphologies. While assemblies regulated by chemical reaction cycles gained traction, the concept of reciprocal coupling is under-explored. In this work, we provide two molecular design strategies to tweak the degree of reciprocal coupling between the assembly and reaction cycle. The strategies involve spacing the chemically active site away from the assembly or burying it into the assembly. We envision that design strategies facilitate the creation of reciprocally coupled and, by extension, dynamic supramolecular materials in the future.
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Affiliation(s)
- Xiaoyao Chen
- Department of Chemistry, School of Natural Sciences, Technical University of Munich Lichtenbergstrasse 4 85748 Garching bei München Germany
| | - Brigitte A K Kriebisch
- Department of Chemistry, School of Natural Sciences, Technical University of Munich Lichtenbergstrasse 4 85748 Garching bei München Germany
| | - Alexander M Bergmann
- Department of Chemistry, School of Natural Sciences, Technical University of Munich Lichtenbergstrasse 4 85748 Garching bei München Germany
| | - Job Boekhoven
- Department of Chemistry, School of Natural Sciences, Technical University of Munich Lichtenbergstrasse 4 85748 Garching bei München Germany
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6
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Tanada M, Tamiya M, Matsuo A, Chiyoda A, Takano K, Ito T, Irie M, Kotake T, Takeyama R, Kawada H, Hayashi R, Ishikawa S, Nomura K, Furuichi N, Morita Y, Kage M, Hashimoto S, Nii K, Sase H, Ohara K, Ohta A, Kuramoto S, Nishimura Y, Iikura H, Shiraishi T. Development of Orally Bioavailable Peptides Targeting an Intracellular Protein: From a Hit to a Clinical KRAS Inhibitor. J Am Chem Soc 2023. [PMID: 37463267 DOI: 10.1021/jacs.3c03886] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Cyclic peptides as a therapeutic modality are attracting a lot of attention due to their potential for oral absorption and accessibility to intracellular tough targets. Here, starting with a drug-like hit discovered using an mRNA display library, we describe a chemical optimization that led to the orally available clinical compound known as LUNA18, an 11-mer cyclic peptide inhibitor for the intracellular tough target RAS. The key findings are as follows: (i) two peptide side chains were identified that each increase RAS affinity over 10-fold; (ii) physico-chemical properties (PCP) including Clog P can be adjusted by side-chain modification to increase membrane permeability; (iii) restriction of cyclic peptide conformation works effectively to adjust PCP and improve bio-activity; (iv) cellular efficacy was observed in peptides with a permeability of around 0.4 × 10-6 cm/s or more in a Caco-2 permeability assay; and (v) while keeping the cyclic peptide's main-chain conformation, we found one example where the RAS protein structure was changed dramatically through induced-fit to our peptide side chain. This study demonstrates how the chemical optimization of bio-active peptides can be achieved without scaffold hopping, much like the processes for small molecule drug discovery that are guided by Lipinski's rule of five. Our approach provides a versatile new strategy for generating peptide drugs starting from drug-like hits.
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Affiliation(s)
- Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Aya Chiyoda
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Koji Takano
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Toshiya Ito
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tomoya Kotake
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hatsuo Kawada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuji Hayashi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shiho Ishikawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Noriyuki Furuichi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yuya Morita
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Mirai Kage
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Satoshi Hashimoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Keiji Nii
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Sase
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kazuhiro Ohara
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Ohta
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yoshikazu Nishimura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Takuya Shiraishi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
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7
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Schweitzer-Stenner R. The relevance of short peptides for an understanding of unfolded and intrinsically disordered proteins. Phys Chem Chem Phys 2023; 25:11908-11933. [PMID: 37096579 DOI: 10.1039/d3cp00483j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Over the last thirty years the unfolded state of proteins has attracted considerable interest owing to the discovery of intrinsically disordered proteins which perform a plethora of functions despite resembling unfolded proteins to a significant extent. Research on both, unfolded and disordered proteins has revealed that their conformational properties can deviate locally from random coil behavior. In this context results from work on short oligopeptides suggest that individual amino acid residues sample the sterically allowed fraction of the Ramachandran plot to a different extent. Alanine has been found to exhibit a peculiarity in that it has a very high propensity for adopting polyproline II like conformations. This Perspectives article reviews work on short peptides aimed at exploring the Ramachandran distributions of amino acid residues in different contexts with experimental and computational means. Based on the thus provided overview the article discussed to what extent short peptides can serve as tools for exploring unfolded and disordered proteins and as benchmarks for the development of a molecular dynamics force field.
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8
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Das NR, Chaudhury KN, Pal D. Improved NMR-data-compliant protein structure modeling captures context-dependent variations and expands the scope of functional inference. Proteins 2023; 91:412-435. [PMID: 36287124 DOI: 10.1002/prot.26439] [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: 05/10/2022] [Revised: 09/12/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy can reveal conformational states of a protein in physiological conditions. However, sparsely available NMR data for a protein with large degrees of freedom can introduce structural artifacts in the built models. Currently used state-of-the-art methods deriving protein structure and conformation from NMR deploy molecular dynamics (MD) coupled with simulated annealing for building models. We provide an alternate graph-based modeling approach, where we first build substructures from NMR-derived distance-geometry constraints combined in one shot to form the core structure. The remaining molecule with inadequate data is modeled using a hybrid approach respecting the observed distance-geometry constraints. One-shot structure building is rarely undertaken for large and sparse data systems, but our data-driven bottom-up approach makes this uniquely feasible by suitable partitioning of the problem. A detailed comparison of select models with state-of-art methods reveals differences in the secondary structure regions wherein the correctness of our models is confirmed by NMR data. Benchmarking of 106 protein-folds covering 38-282 length structures shows minimal experimental-constraint violations while conforming to other structure quality parameters such as the proper folding, steric clash, and torsion angle violation based on Ramachandran plot criteria. Comparative MD studies using select protein models from a state-of-art method and ours under identical experimental parameters reveal distinct conformational dynamics that could be attributed to protein structure-function. Our work is thus useful in building enhanced NMR-evidence-based models that encapsulate the contextual secondary and tertiary structure variations present during the experimentation and expand the scope of functional inference.
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Affiliation(s)
- Niladri R Das
- IISc Mathematics Initiative, Indian Institute of Science, Bangalore, India.,Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Kunal N Chaudhury
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
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9
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Morita D, Asa M, Sugita M. Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules. Int Immunol 2023; 35:7-17. [PMID: 36053252 DOI: 10.1093/intimm/dxac046] [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: 07/17/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).
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Affiliation(s)
- Daisuke Morita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Minori Asa
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiko Sugita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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10
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Safiriyu AA, Mulchandani V, Anakkacheri MN, Pal D, Das Sarma J. Proline-Proline Dyad in the Fusion Peptide of the Murine β-Coronavirus Spike Protein's S2 Domain Modulates Its Neuroglial Tropism. Viruses 2023; 15:215. [PMID: 36680255 PMCID: PMC9865228 DOI: 10.3390/v15010215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
The β-Coronavirus mouse hepatitis virus (MHV-A59)-RSA59 has a patent stretch of fusion peptide (FP) containing two consecutive central prolines (PP) in the S2 domain of the Spike protein. Our previous studies compared the PP-containing fusogenic-demyelinating strain RSA59(PP) to its one proline-deleted mutant strain RSA59(P) and one proline-containing non-fusogenic non-demyelinating parental strain RSMHV2(P) to its one proline inserted mutant strain RSMHV2(PP). These studies highlighted the crucial role of PP in fusogenicity, hepato-neuropathogenesis, and demyelination. Computational studies combined with biophysical data indicate that PP at the center of the FP provides local rigidity while imparting global fluctuation to the Spike protein that enhances the fusogenic properties of RSA59(PP) and RSMHV2(PP). To elaborate on the understanding of the role of PP in the FP of MHV, the differential neuroglial tropism of the PP and P mutant strains was investigated. Comparative studies demonstrated that PP significantly enhances the viral tropism for neurons, microglia, and oligodendrocytes. PP, however, is not essential for viral tropism for either astroglial or oligodendroglial precursors or the infection of meningeal fibroblasts in the blood-brain and blood-CSF barriers. PP in the fusion domain is critical for promoting gliopathy, making it a potential region for designing antivirals for neuro-COVID therapy.
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Affiliation(s)
- Abass Alao Safiriyu
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Vaishali Mulchandani
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Mohammed Nahaf Anakkacheri
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru 560012, India
| | - Jayasri Das Sarma
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
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11
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Phan TM, Schmit JD. Conformational entropy limits the transition from nucleation to elongation in amyloid aggregation. Biophys J 2022; 121:2931-2939. [PMID: 35778843 PMCID: PMC9388551 DOI: 10.1016/j.bpj.2022.06.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 11/30/2022] Open
Abstract
The formation of β-sheet rich amyloid fibrils in Alzheimer's disease and other neurodegenerative disorders is limited by a slow nucleation event. To understand the initial formation of β-sheets from disordered peptides, we used all-atom simulations to parameterize a lattice model that treats each amino acid as a binary variable with β and non-β states. We show that translational and conformational entropy give the nascent β-sheet an anisotropic surface tension which can be used to describe the nucleus with two-dimensional Classical Nucleation Theory. Since translational entropy depends on concentration, the aspect ratio of the critical β-sheet changes with protein concentration. Our model explains the transition from the nucleation phase to elongation as the point where the β-sheet core becomes large enough to overcome the conformational entropy cost to straighten the terminal molecule. At this point the β-strands in the nucleus spontaneously elongate, which results in a larger binding surface to capture new molecules. These results suggest that nucleation is relatively insensitive to sequence differences in co-aggregation experiments because the nucleus only involves a small portion of the peptide.
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Affiliation(s)
- Tien M Phan
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA.
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12
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Meriño-Cabrera Y, Castro JS, de Almeida Barros R, da Silva Junior NR, de Oliveira Ramos H, de Almeida Oliveira MG. Arginine-containing dipeptides decrease affinity of gut trypsins and compromise soybean pest development. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 184:105107. [PMID: 35715046 DOI: 10.1016/j.pestbp.2022.105107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
The design and production of molecules capable of mimicking the binding or/and functional sites of proteins inhibitors represent a promising strategy for the exploration and modulation of gut trypsin function in insect pests, specifically Lepidoptera. Here, for the first time, we characterized the trypsin activity present in the gut, performance and development of Anticarsia gemmatalis (Lepidoptera: Noctuidae) larvae when exposed to arginine-containing dipeptides. In silico assessment showed that arginine-containing dipeptides have a greater affinity for the active site of A. gemmatalis trypsins than lysine-containing peptides due to the presence of the double-charged guanidinium group that enhances the interaction at the S1 subsite of trypsins. Furthermore, the inhibitory and anti-insect potential of the peptides was demonstrated through kinetic and larval life cycle parameters, respectively. These dipeptides showed structural stability, binding to the active site, corroborated in vitro (competitive inhibition), and significant reduction of trypsin enzyme activity in the gut, survival, and weight of the A. gemmatalis larvae. Our findings reinforce the idea that small peptides are promising candidates for lepidopteran pest management. The optimization of DI2 and DI1 peptides, enhancing uptake and affinity to trypsins, may turn the use of these molecules feasible in agriculture.
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Affiliation(s)
- Yaremis Meriño-Cabrera
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - José Severiche Castro
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Rafael de Almeida Barros
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Neilier Rodrigues da Silva Junior
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Humberto de Oliveira Ramos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Maria Goreti de Almeida Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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13
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Safiriyu AA, Singh M, Kishore A, Mulchandani V, Maity D, Behera A, Sinha B, Pal D, Das Sarma J. Two Consecutive Prolines in the Fusion Peptide of Murine β-Coronavirus Spike Protein Predominantly Determine Fusogenicity and May Be Essential but Not Sufficient to Cause Demyelination. Viruses 2022; 14:v14040834. [PMID: 35458565 PMCID: PMC9031231 DOI: 10.3390/v14040834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Combined in silico, in vitro, and in vivo comparative studies between isogenic-recombinant Mouse-Hepatitis-Virus-RSA59 and its proline deletion mutant, revealed a remarkable contribution of centrally located two consecutive prolines (PP) from Spike protein fusion peptide (FP) in enhancing virus fusogenic and hepato-neuropathogenic potential. To deepen our understanding of the underlying factors, we extend our studies to a non-fusogenic parental virus strain RSMHV2 (P) with a single proline in the FP and its proline inserted mutant, RSMHV2 (PP). Comparative in vitro and in vivo studies between virus strains RSA59(PP), RSMHV2 (P), and RSMHV2 (PP) in the FP demonstrate that the insertion of one proline significantly resulted in enhancing the virus fusogenicity, spread, and consecutive neuropathogenesis. Computational studies suggest that the central PP in Spike FP induces a locally ordered, compact, and rigid structure of the Spike protein in RSMHV2 (PP) compared to RSMHV2 (P), but globally the Spike S2-domain is akin to the parental strain RSA59(PP), the latter being the most flexible showing two potential wells in the energy landscape as observed from the molecular dynamics studies. The critical location of two central prolines of the FP is essential for fusogenicity and pathogenesis making it a potential site for designing antiviral.
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Affiliation(s)
- Abass Alao Safiriyu
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India; (A.A.S.); (M.S.); (A.K.); (V.M.); (A.B.); (B.S.)
| | - Manmeet Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India; (A.A.S.); (M.S.); (A.K.); (V.M.); (A.B.); (B.S.)
| | - Abhinoy Kishore
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India; (A.A.S.); (M.S.); (A.K.); (V.M.); (A.B.); (B.S.)
| | - Vaishali Mulchandani
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India; (A.A.S.); (M.S.); (A.K.); (V.M.); (A.B.); (B.S.)
| | - Dibyajyoti Maity
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru 560012, India; (D.M.); (D.P.)
| | - Amrutamaya Behera
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India; (A.A.S.); (M.S.); (A.K.); (V.M.); (A.B.); (B.S.)
| | - Bidisha Sinha
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India; (A.A.S.); (M.S.); (A.K.); (V.M.); (A.B.); (B.S.)
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru 560012, India; (D.M.); (D.P.)
| | - Jayasri Das Sarma
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India; (A.A.S.); (M.S.); (A.K.); (V.M.); (A.B.); (B.S.)
- Correspondence:
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14
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Khechinashvili NN, Kondratyev MS, Polozov RV. Thermodynamics of globular protein native structure. J Biomol Struct Dyn 2022; 41:3218-3221. [PMID: 35345984 DOI: 10.1080/07391102.2022.2046637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The temperature dependence of the partial heat capacity of the native protein structure in an aqueous solution has been analyzed. It is shown that the strictly linear temperature dependence is due to the contributions of the vibrational and conformational components, which indicates volume consistensy and the absence of conformational transitions up to the main two-state transition. The two-level structural and functional organization of the protein three-dimensional structure are considered in relation to the energy and conformational entropy properties in accordance with the principles of the organization of the protein macromolecule.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Maxim S Kondratyev
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Robert V Polozov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
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15
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Gao X, Zhao Q, Wei J, Zhang H. Study on the Potential Distribution of Leptinotarsa decemlineata and Its Natural Enemy Picromerus bidens Under Climate Change. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.786436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Colorado potato beetle (CPB), scientifically known as Leptinotarsa decemlineata, is a destructive quarantine pest that has invaded more than 40 countries and regions worldwide. It causes a 20–100% reduction in plant production, leading to severe economic losses. Picromerus bidens L. is a predatory insect that preys on CPB. This study used the MaxEnt model to predict the current and future potential distribution areas of CPB and P. bidens under different climatic scenarios to determine the possibility of using P. bidens as a natural enemy to control CPB. The possible introduction routes of CPB and P. bidens were subsequently predicted by combining their potential distribution with the current distribution of airports and ports. Notably, the potential distribution area of P. bidens was similar to that of CPB, suggesting that P. bidens could be used as a natural enemy to control CPB. Future changes in the suitable growth areas of CPB under different climate scenarios increased and decreased but were insignificant, while those of P. bidens decreased. Consequently, a reduction of the suitable habitats of P. bidens may cause a decrease in its population density, leading to a lack of adequate and timely prevention and control of invasive pests. Active measures should thus be enacted to minimize global warming and protect biodiversity. This study provides a theoretical basis and data support for early warning, monitoring, and control of the CPB spread.
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16
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Aoki D, Miyake A, Tachaboonyakiat W, Ajiro H. Remarkable diastereomeric effect on thermoresponsive behavior of polyurethane based on lysine and tartrate ester derivatives. RSC Adv 2021; 11:35607-35613. [PMID: 35493186 PMCID: PMC9043254 DOI: 10.1039/d1ra05877k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/23/2021] [Indexed: 11/24/2022] Open
Abstract
This study describes the long-distance diastereomeric effect on thermoresponsive properties in water-soluble diastereomeric polyurethanes (PUs) composed of an l-lysine ethyl ester diisocyanate and a trimethylene glycol l-/d-tartrate ester, which have differences in spatial arrangements of the ethyl esters in the mirror image. The PUs based on l-lysine and l-/d-tartrate ester, named l-PU and d-PU, were synthesized with various number average molecular weights from 4700 to 13 100. In turbidimetry, l-PU showed a steep phase transition from 100%T to 0%T within about 10 °C at 4 g L−1, whereas d-PU did not change completely to 0%T transmittance even at 80 °C at 4 g L−1. In addition, the thermoresponsive properties of l-PU were less affected by concentration than those of d-PU. This long-distance diastereomeric effect on thermoresponsive behavior between l-PU and d-PU appeared in common among 6 samples with 4700 to 13 100 number average molecular weight. In the dynamic light scattering experiments at each transmittance, the hydrodynamic diameter (Dh) of l-PU increased up to 1000 nm, while the Dh of d-PU remained almost at 200–300 nm. The C
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O stretching vibration of FT-IR spectra showed that d-PU has more hydrogen-bonded ester groups than L-PU. Thus, we speculated that the difference in the retention of polymer chains in the micelle to promote intermicellar bridging generates the long-distance diastereomeric effect. The long-distance diastereomeric effect on thermoresponsive properties in a polyurethane system consisting of chiral monomers was reported.![]()
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Affiliation(s)
- Daisuke Aoki
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Akihiro Miyake
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Wanpen Tachaboonyakiat
- Department of Materials Science, Faculty of Science, Chulalongkorn University Phayathai, Pathumwan Bangkok 10330 Thailand
| | - Hiroharu Ajiro
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan .,Data Science Center, Nara Institute of Science and Technology 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
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17
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Rao SJA, Shetty NP. Evolutionary selectivity of amino acid is inspired from the enhanced structural stability and flexibility of the folded protein. Life Sci 2021; 281:119774. [PMID: 34197884 DOI: 10.1016/j.lfs.2021.119774] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/18/2022]
Abstract
AIM The present study attempts to decipher the site-specific amino acid alterations at certain positions experiencing preferential selectivity and their effect on proteins' stability and flexibility. The study examines the selection preferences by considering pair-wise non-bonded interaction energies of adjacent and interacting amino acids present at the interacting site, along with their evolutionary history. MATERIALS AND METHODS For the study, variations in the interacting residues of spike protein (S-Protein) receptor-binding domain (RBD) of different coronaviruses were examined. The MD simulation trajectory analysis revealed that, though all the variants studied were structurally stable at their native and bound confirmations, the RBD of 2019-nCoV/SARS-CoV-2 was found to be more flexible and more dynamic. Furthermore, a noticeable change observed in the non-bonded interaction energies of the amino acids interacting with the receptor corroborated their selection at respective positions. KEY FINDINGS The conformational changes exerted by the altered amino acids could be the reason for a broader range of interacting receptors among the selected proteins. SIGNIFICANCE The results envisage a strong indication that the residue selection at certain positions is governed by a well-orchestrated feedback mechanism, which follows increased stability and flexibility in the folded structure compared to its evolutionary predecessor.
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Affiliation(s)
- S J Aditya Rao
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India.
| | - Nandini P Shetty
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
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18
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Pal D. Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity. J Struct Biol 2021; 213:107713. [PMID: 33662570 PMCID: PMC7919542 DOI: 10.1016/j.jsb.2021.107713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 01/30/2023]
Abstract
The high SARS-CoV-2 reproductive number driving the COVID-19 pandemic has been a mystery. Our recent in vitro, and in vivo coronaviral pathogenesis studies involving Mouse Hepatitis Virus (MHV-A59) suggest a crucial role for a small host membrane-virus contact initiator region of the Spike protein, called the fusion peptide that enhances the virus fusogenicity and infectivity. Here I study the Spike from five human β-coronaviruses (HCoV) including the SARS-CoV-2, and MHV-A59 for comparison. The structural and dynamics analyses of the Spike show that its fusion loop spatially organizes three fusion peptides contiguous to each other to synergistically trigger the virus-host membrane fusion process. I propose a Contact Initiation Model based on the architecture of the Spike quaternary structure that explains the obligatory participation of the fusion loop in the initiation of the host membrane contact for the virus fusion process. Among all the HCoV Spikes in this study, SARS-CoV-2 has the most hydrophobic surface and the extent of hydrophobicity correlates with the reproductive number and infectivity of the other HCoV. Comparison between results from standard and replica exchange molecular dynamics reveal the unique physicochemical properties of the SARS-CoV-2 fusion peptides, accrued in part from the presence of consecutive prolines that impart backbone rigidity which aids the virus fusogenicity. The priming of the Spike by its cleavage and subsequent fusogenic conformational transition steered by the fusion loop may be critical for the SARS-CoV-2 spread. The importance of the fusion loop makes it an apt target for anti-virals and vaccine candidates.
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Affiliation(s)
- Debnath Pal
- Indian Institute of Science, Bengaluru 560012, India.
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19
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Blanár E, Leitgeb B. Studying the helical conformations of aspereline peptides. Chem Biol Drug Des 2021; 97:1029-1037. [PMID: 33638250 DOI: 10.1111/cbdd.13834] [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: 09/20/2020] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 11/29/2022]
Abstract
Asperelines are short-sequence peptaibol molecules, and these peptides composed of 10 residues were isolated from the Trichoderma asperellum. In our study, a detailed structural characterization was performed on the asperelines by means of molecular dynamics methods. For the aspereline peptides, the occurrence of various secondary structural elements (i.e. β-turns and helical structures) was investigated along their entire sequences. The results derived from the simulated annealing calculations led to the observations that in the case of asperelines, the types I, III and III' β-turn structures, as well as their stabilizing i ← i+3 H-bonds appeared. However, beside the different β-turns, shorter or longer helical structures were also detected. Based on the results obtained by the molecular dynamics simulations, it was concluded that the three-dimensional structure of aspereline peptides could be characterized by helical conformations (i.e. 310 - and α-helix). Nevertheless, on the basis of individual molecular dynamics trajectories, it was observed that the asperelines could adopt not only the right-handed, but also the left-handed helical structures.
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Affiliation(s)
- Eszter Blanár
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Balázs Leitgeb
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
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20
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Kriebisch BAK, Jussupow A, Bergmann AM, Kohler F, Dietz H, Kaila VRI, Boekhoven J. Reciprocal Coupling in Chemically Fueled Assembly: A Reaction Cycle Regulates Self-Assembly and Vice Versa. J Am Chem Soc 2020; 142:20837-20844. [PMID: 33237773 DOI: 10.1021/jacs.0c10486] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In biology, self-assembly of proteins and energy-consuming reaction cycles are intricately coupled. For example, tubulin is activated and deactivated for assembly by a guanosine triphosphate (GTP)-driven reaction cycle, and the emerging microtubules catalyze this reaction cycle by changing the microenvironment of the activated tubulin. Recently, synthetic analogs of chemically fueled assemblies have emerged, but examples in which assembly and reaction cycles are reciprocally coupled remain rare. In this work, we report a peptide that can be activated and deactivated for self-assembly. The emerging assemblies change the microenvironment of their building blocks, which consequently accelerate the rates of building block deactivation and reactivation. We quantitatively understand the mechanisms at play, and we are thus able to tune the catalysis by molecular design of the peptide precursor.
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Affiliation(s)
- Brigitte A K Kriebisch
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Alexander Jussupow
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Alexander M Bergmann
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Fabian Kohler
- Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Hendrik Dietz
- Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Ville R I Kaila
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.,Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2a, 85748 Garching, Germany
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21
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Khatri B, Majumder P, Nagesh J, Penmatsa A, Chatterjee J. Increasing protein stability by engineering the n → π* interaction at the β-turn. Chem Sci 2020; 11:9480-9487. [PMID: 34094214 PMCID: PMC8161691 DOI: 10.1039/d0sc03060k] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abundant n → π* interactions between adjacent backbone carbonyl groups, identified by statistical analysis of protein structures, are predicted to play an important role in dictating the structure of proteins. However, experimentally testing the prediction in proteins has been challenging due to the weak nature of this interaction. By amplifying the strength of the n → π* interaction via amino acid substitution and thioamide incorporation at a solvent exposed β-turn within the GB1 proteins and Pin 1 WW domain, we demonstrate that an n → π* interaction increases the structural stability of proteins by restricting the ϕ torsion angle. Our results also suggest that amino acid side-chain identity and its rotameric conformation play an important and decisive role in dictating the strength of an n → π* interaction. Amino acid residues adopt a right-handed α-helical conformation with increasing strength of the n → π* interaction. We also demonstrate a direct consequence of n → π* interactions on enhancing the structural stability of proteins.![]()
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Puja Majumder
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
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22
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Vermeyen T, Merten C. Solvation and the secondary structure of a proline-containing dipeptide: insights from VCD spectroscopy. Phys Chem Chem Phys 2020; 22:15640-15648. [PMID: 32617548 DOI: 10.1039/d0cp02283g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study we investigate the IR and VCD spectra of the diastereomeric dipeptide Boc-Pro-Phe-(n-propyl) 1 in chloroform-d1 (CDCl3) and the strongly hydrogen bonding solvent dimethylsulfoxide-d6 (DMSO-d6). From comparison of the experimental spectra, the amide II spectral region is identified as marker signature for the stereochemistry of the dipeptide: the homochiral LL-1 features a (+/-)-pattern in the amide II region of the VCD spectrum, while the amide II signature of the diastereomer LD-1 is inverted. Computational analysis of the IR and VCD spectra of LL-1 reveals that the experimentally observed amide II signature is characteristic for a βI-turn structure of the peptide. Likewise, the inverted pattern found for LD-1 arises from a βII-turn structure of the dipeptide. Following a micro-solvation approach, the experimental spectra recorded in DMSO-d6 are computationally well reproduced by considering only a single solvent molecule in a hydrogen bond with N-H groups. Considering a second solvent molecule, which would lead to a cleavage of intramolecular hydrogen bonds in 1, is found to give a significantly worse match with the experiment. Hence, the detailed computational analysis of the spectra of LL- and LD-1 recorded in DMSO-d6 confirms that the intramolecular hydrogen bonding pattern, that stabilizes the β-turns and other conformations of LL- and LD-1 in apolar solvents, remains intact. Our findings also show that it is essential to consider solvation explicitly in the analysis of the IR and VCD spectra of dipeptides in strongly hydrogen bonding solvents. As the solute-solvent interactions affect both conformational preferences and spectral signatures, it is also demonstrated that this inclusion of solvent molecules cannot be circumvented by applying fitting procedures to non-solvated structures.
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Affiliation(s)
- Tom Vermeyen
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany. and University of Antwerp, Department of Chemistry, MolSpec Group, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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23
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Pal D, Sahu S, Banerjee R. New facets of larger Nest motifs in proteins. Proteins 2020; 88:1413-1422. [PMID: 32519388 DOI: 10.1002/prot.25961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/06/2020] [Indexed: 11/07/2022]
Abstract
The Nest is a concave-shaped structural motif in proteins formed by consecutive enantiomeric left-handed (L) and right-handed (R) helical conformation of the backbone. This important motif subsumes many turn and helix capping structures and binds electron-rich ligands. Simple Nests are either RL or LR. Larger Nests (>2 residues long) may be RLR, LRL, RLRL, and so forth, being considered as composed of overlapping simple Nests. The larger Nests remain under-explored despite their widely known contributions to protein function. In our study, we address whether the recurrence of enantiomeric geometry in the larger Nests constrains the peptide backbone such that distinct compositional and conformational preferences are seen compared to simple Nests. Our analysis reveals the critical role of the L helical torsion angle in the formation of larger Nests. This can be observed through the higher propensity of residue or secondary structure combinations in LR and LRL backbone conformation in comparison to RL or RLR, although LR/LRL is considerably lower by occurrence. We also find that the most abundant doublets and triplets in Nests have a propensity for particular secondary structures, suggesting a strong sequence-structure relationship in the larger Nest. Overall, our analysis corroborates distinct features of simple and the larger Nests. Such insights would be helpful towards in-vitro design of peptides and peptidomimetic studies.
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Affiliation(s)
- Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Subhankar Sahu
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Raja Banerjee
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
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24
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Dhar J, Kishore R, Chakrabarti P. Delineation of a new structural motif involving NHN γ-turn. Proteins 2019; 88:431-439. [PMID: 31587358 DOI: 10.1002/prot.25820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
Abstract
Macromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non-redundant protein chains reveals the existence of a three-residue, (i - 1) to (i + 1), structural motif, having two hydrogen-bonded five-membered pseudo rings (the first, an NH···OC involving the first residue, and the second being NH∙∙∙N involving the last two residues), separated by a peptide bond. There could be an additional hydrogen bond between the side-chain at (i-1) and the main-chain NH of (i + 1). The average backbone torsion angles of -76(±21)° and - 12(±17)° at i creates a tight turn in the polypeptide chain, akin to a γ-turn. Indeed, a search of three-residue fragments with restriction on the terminal Cα ···Cα distance and the existence of the two pseudo rings on either side revealed the presence 14 846 cases of a variant, termed NHN γ-turn, distinct from the NHO γ-turn (2032 cases) that has traditionally been characterized by the presence of NHO hydrogen bond linking the terminal main-chain atoms. As in the latter, the newly identified γ-turns are also of two types-classical and inverse, occurring in the ratio of 1:6. The propensities of residues to occur in these turns and their secondary structural features have been enumerated. An understanding of these turns would be useful for structure prediction and loop modeling, and may serve as models to represent some of the unfolded state or disordered region in proteins.
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Affiliation(s)
- Jesmita Dhar
- Bioinformatics Centre, Bose Institute, Kolkata, India
| | - Raghuvansh Kishore
- Department of Zoology and Department of Biotechnology, Mizoram University, Aizawl, India
| | - Pinak Chakrabarti
- Bioinformatics Centre, Bose Institute, Kolkata, India.,Department of Biochemistry, Bose Institute, Kolkata, India
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25
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Ahmed MH, Catalano C, Portillo SC, Safo MK, Neel Scarsdale J, Kellogg GE. 3D interaction homology: The hydropathic interaction environments of even alanine are diverse and provide novel structural insight. J Struct Biol 2019; 207:183-198. [DOI: 10.1016/j.jsb.2019.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/12/2019] [Accepted: 05/17/2019] [Indexed: 01/23/2023]
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26
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Kato T, Kishimoto S, Asano A, Doi M. Crystal structure of N-{ N-[ N-( tert-but-oxy-carbon-yl)-l-α-aspart-yl]-l-α-aspart-yl}-l-α-aspartic acid 1 4,2 4,3 4-trimethyl ester 3 1-2-oxo-2-phenyl-ethyl ester {Boc-[Asp(OMe)] 3-OPac}. Acta Crystallogr E Crystallogr Commun 2019; 75:585-588. [PMID: 31110791 PMCID: PMC6505608 DOI: 10.1107/s2056989019004596] [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: 03/08/2019] [Accepted: 04/04/2019] [Indexed: 11/10/2022]
Abstract
In the title homotripeptide {Boc-[Asp(OMe)]3-OPac}, C28H37N3O13, all peptide bonds adopt an s-trans conformation with respect to the N-H and C=O groups. In the crystal, N-H⋯O hydrogen bonds result in an infinite parallel β-sheet structure running along the b-axis direction. The Boc protecting group at the N-terminus of the peptide is disordered over two sites with occupancy factors of 0.504 (5) and 0.496 (5).
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Affiliation(s)
- Takuma Kato
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Saki Kishimoto
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Akiko Asano
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
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27
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Singh M, Kishore A, Maity D, Sunanda P, Krishnarjuna B, Vappala S, Raghothama S, Kenyon LC, Pal D, Das Sarma J. A proline insertion-deletion in the spike glycoprotein fusion peptide of mouse hepatitis virus strongly alters neuropathology. J Biol Chem 2019; 294:8064-8087. [PMID: 30824541 DOI: 10.1074/jbc.ra118.004418] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 02/24/2019] [Indexed: 11/06/2022] Open
Abstract
Fusion peptides (FPs) in spike proteins are key players mediating early events in cell-to-cell fusion, vital for intercellular viral spread. A proline residue located at the central FP region has often been suggested to have a distinctive role in this fusion event. The spike glycoprotein from strain RSA59 (PP) of mouse hepatitis virus (MHV) contains two central, consecutive prolines in the FP. Here, we report that deletion of one of these proline residues, resulting in RSA59 (P), significantly affected neural cell syncytia formation and viral titers postinfection in vitro Transcranial inoculation of C57Bl/6 mice with RSA59 (PP) or RSA59 (P) yielded similar degrees of necrotizing hepatitis and meningitis, but only RSA59 (PP) produced widespread encephalitis that extended deeply into the brain parenchyma. By day 6 postinfection, both virus variants were mostly cleared from the brain. Interestingly, inoculation with the RSA59 (P)-carrying MHV significantly reduced demyelination at the chronic stage. We also found that the presence of two consecutive prolines in FP promotes a more ordered, compact, and rigid structure in the spike protein. These effects on FP structure were due to proline's unique stereochemical properties intrinsic to its secondary amino acid structure, revealed by molecular dynamics and NMR experiments. We therefore propose that the differences in the severity of encephalitis and demyelination between RSA59 (PP) and RSA59 (P) arise from the presence or absence, respectively, of the two consecutive prolines in FP. Our studies define a structural determinant of MHV entry in the brain parenchyma important for altered neuropathogenesis.
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Affiliation(s)
- Manmeet Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Abhinoy Kishore
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | | | | | | | - Sreeparna Vappala
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | | | - Lawrence C Kenyon
- Department of Anatomy, Pathology, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru 560012, India.
| | - Jayasri Das Sarma
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India.
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28
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Rose GD. Ramachandran maps for side chains in globular proteins. Proteins 2019; 87:357-364. [PMID: 30629766 DOI: 10.1002/prot.25656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 12/30/2018] [Indexed: 11/05/2022]
Abstract
The Ramachandran plot for backbone ϕ,ψ-angles in a blocked monopeptide has played a central role in understanding protein structure. Curiously, a similar analysis for side chain χ-angles has been comparatively neglected. Instead, efforts have focused on compiling various types of side chain libraries extracted from proteins of known structure. Departing from this trend, the following analysis presents backbone-based maps of side chains in blocked monopeptides. As in the original ϕ,ψ-plot, these maps are derived solely from hard-sphere steric repulsion. Remarkably, the side chain biases exhibit marked similarities to corresponding biases seen in high-resolution protein structures. Consequently, some of the entropic cost for side chain localization in proteins is prepaid prior to the onset of folding events because conformational bias is built into the chain at the covalent level. Furthermore, side chain conformations are seen to experience fewer steric restrictions for backbone conformations in either the α or β basins, those map regions where repetitive ϕ,ψ-angles result in α-helices or strands of β-sheet, respectively. Here, these α and β basins are entropically favored for steric reasons alone; a blocked monopeptide is too short to accommodate the peptide hydrogen bonds that stabilize repetitive secondary structure. Thus, despite differing energetics, α/β-basins are favored for both monopeptides and repetitive secondary structure, underpinning an energetically unfrustrated compatibility between these two levels of protein structure.
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Affiliation(s)
- George D Rose
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
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29
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Alonso JL, Peña I, López JC, Alonso ER, Vaquero V. The Shape of the Simplest Non-proteinogenic Amino Acid α-Aminoisobutyric Acid (Aib). Chemistry 2019; 25:2288-2294. [DOI: 10.1002/chem.201805038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/09/2018] [Indexed: 11/12/2022]
Affiliation(s)
- José L. Alonso
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorio de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Isabel Peña
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorio de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Juan C. López
- Departamento de Química Física e Inorgánica; Facultad de, Ciencias; Universidad de Valladolid; 47011 Valladolid Spain
| | - Elena R. Alonso
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorio de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Vanesa Vaquero
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorio de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
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30
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López-García P, Goktas M, Bergues-Pupo AE, Koksch B, Varón Silva D, Blank KG. Structural determinants of coiled coil mechanics. Phys Chem Chem Phys 2019; 21:9145-9149. [PMID: 31016294 DOI: 10.1039/c9cp00665f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The natural abundance of coiled coil (CC) motifs in the cytoskeleton and the extracellular matrix suggests that CCs play a crucial role in the bidirectional mechanobiochemical signaling between cells and the matrix. Their functional importance and structural simplicity has allowed the development of numerous applications, such as protein-origami structures, drug delivery systems and biomaterials. With the goal of establishing CCs as nanomechanical building blocks, we investigated the importance of helix propensity and hydrophobic core packing on the mechanical stability of 4-heptad CC heterodimers. Using single-molecule force spectroscopy, we show that both parameters determine the force-induced dissociation in shear loading geometry; however, with different effects on the energy landscape. Decreasing the helix propensity lowers the transition barrier height, leading to a concomitant decrease in the distance to the transition state. In contrast, a less tightly packed hydrophobic core increases the distance to the transition state. We propose that this originates from a larger side chain dynamics, possible water intrusion at the interface as well as differences in solvation of the hydrophobic amino acids at the transition state. In conclusion, the different contributions of helix propensity and hydrophobic core packing need to be considered when tuning the mechanical properties of CCs for applications.
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Affiliation(s)
- Patricia López-García
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Science-Park Potsdam Golm, 14424 Potsdam, Germany.
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31
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Beckett D, El-Baba TJ, Clemmer DE, Raghavachari K. Electronic Energies Are Not Enough: An Ion Mobility-Aided, Quantum Chemical Benchmark Analysis of H+GPGG Conformers. J Chem Theory Comput 2018; 14:5406-5418. [DOI: 10.1021/acs.jctc.8b00648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Tarick J. El-Baba
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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32
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Hiraoka S. Unresolved Issues that Remain in Molecular Self-Assembly. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180008] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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33
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Chiral self-sorting process in the self-assembly of homochiral coordination cages from axially chiral ligands. Commun Chem 2018. [DOI: 10.1038/s42004-018-0020-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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34
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Synthesis of cis- and trans-(±)-3-mercaptoproline and pipecolic acid derivatives via thio-Michael addition. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.03.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Kotynia A, Pap JS, Brasun J. The binding abilities of homodetic cyclic His-peptides toward copper ions. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.07.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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36
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Voronina L, Scutelnic V, Masellis C, Rizzo TR. Can Mutational Analysis Be Used To Assist Structure Determination of Peptides? J Am Chem Soc 2018; 140:2401-2404. [PMID: 29412650 DOI: 10.1021/jacs.7b11302] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mutational analysis is widely used to study the relationship between sequence and structure of proteins and peptides. It is often assumed that substituting a proline with another amino acid "locks" the peptide bond in the trans conformation, allowing only a subset of the initial molecular geometries to be observed. To test this assumption, we assess the result of substituting two prolines in the bradykinin sequence with alanine using field-asymmetric ion mobility spectrometry combined with cryogenic ion spectroscopy in the gas phase. While the structure of the mutant coincides with a part of the conformational space of the original peptide, the higher flexibility of the alanine backbone compared to proline allows it to access additional structures. We conclude that proline-to-nonproline substitutions are helpful to assign structures, but they should be used in conjunction with spectroscopic techniques that allow detailed comparison of the structures of the mutant and the native peptide.
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Affiliation(s)
- Liudmila Voronina
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne, Switzerland
| | - Valeriu Scutelnic
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne, Switzerland
| | - Chiara Masellis
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne, Switzerland
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37
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Kumar S. Prediction of Metal Ion Binding Sites in Proteins from Amino Acid Sequences by Using Simplified Amino Acid Alphabets and Random Forest Model. Genomics Inform 2017; 15:162-169. [PMID: 29307143 PMCID: PMC5769865 DOI: 10.5808/gi.2017.15.4.162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 11/20/2022] Open
Abstract
Metal binding proteins or metallo-proteins are important for the stability of the protein and also serve as co-factors in various functions like controlling metabolism, regulating signal transport, and metal homeostasis. In structural genomics, prediction of metal binding proteins help in the selection of suitable growth medium for overexpression's studies and also help in obtaining the functional protein. Computational prediction using machine learning approach has been widely used in various fields of bioinformatics based on the fact all the information contains in amino acid sequence. In this study, random forest machine learning prediction systems were deployed with simplified amino acid for prediction of individual major metal ion binding sites like copper, calcium, cobalt, iron, magnesium, manganese, nickel, and zinc.
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Affiliation(s)
- Suresh Kumar
- Department of Diagnostic and Allied Health Sciences, Faculty of Health and Life Sciences, Management and Science University, 40100 Shah Alam, Malaysia
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38
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Chadani Y, Niwa T, Izumi T, Sugata N, Nagao A, Suzuki T, Chiba S, Ito K, Taguchi H. Intrinsic Ribosome Destabilization Underlies Translation and Provides an Organism with a Strategy of Environmental Sensing. Mol Cell 2017; 68:528-539.e5. [PMID: 29100053 DOI: 10.1016/j.molcel.2017.10.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/28/2017] [Accepted: 10/06/2017] [Indexed: 01/05/2023]
Abstract
Nascent polypeptides can modulate the polypeptide elongation speed on the ribosome. Here, we show that nascent chains can even destabilize the translating Escherichia coli ribosome from within. This phenomenon, termed intrinsic ribosome destabilization (IRD), occurs in response to a special amino acid sequence of the nascent chain, without involving the release or the recycling factors. Typically, a consecutive array of acidic residues and those intermitted by alternating prolines induce IRD. The ribosomal protein bL31, which bridges the two subunits, counteracts IRD, such that only strong destabilizing sequences abort translation in living cells. We found that MgtL, the leader peptide of a Mg2+ transporter (MgtA), contains a translation-aborting sequence, which sensitizes the ribosome to a decline in Mg2+ concentration and thereby triggers the MgtA-upregulating genetic scheme. Translation proceeds at an inherent risk of ribosomal destabilization, and nascent chain-ribosome complexes can function as a Mg2+ sensor by harnessing IRD.
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Affiliation(s)
- Yuhei Chadani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Takashi Izumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Nobuyuki Sugata
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8565, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8565, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Koreaki Ito
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan.
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
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39
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Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily. Sci Rep 2017; 7:45978. [PMID: 28397787 PMCID: PMC5387724 DOI: 10.1038/srep45978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/07/2017] [Indexed: 02/07/2023] Open
Abstract
Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function.
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40
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Jędrzejewska H, Szumna A. Making a Right or Left Choice: Chiral Self-Sorting as a Tool for the Formation of Discrete Complex Structures. Chem Rev 2017; 117:4863-4899. [PMID: 28277655 DOI: 10.1021/acs.chemrev.6b00745] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This review discusses chiral self-sorting-the process of choosing an interaction partner with a given chirality from a complex mixture of many possible racemic partners. Chiral self-sorting (also known as chiral self-recognition or chiral self-discrimination) is fundamental for creating functional structures in nature and in the world of chemistry because interactions between molecules of the same or the opposite chirality are characterized by different interaction energies and intrinsically different resulting structures. However, due to the similarity between recognition sites of enantiomers and common conformational lability, high fidelity homochiral or heterochiral self-sorting poses a substantial challenge. Chiral self-sorting occurs among natural and synthetic molecules that leads to the amplification of discrete species. The review covers a variety of complex self-assembled structures ranging from aggregates made of natural and racemic peptides and DNA, through artificial functional receptors, macrocyles, and cages to catalytically active metal complexes and helix mimics. The examples involve a plethora of reversible interactions: electrostatic interactions, π-π stacking, hydrogen bonds, coordination bonds, and dynamic covalent bonds. A generalized view of the examples collected from different fields allows us to suggest suitable geometric models that enable a rationalization of the observed experimental preferences and establishment of the rules that can facilitate further design.
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Affiliation(s)
- Hanna Jędrzejewska
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
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41
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Sasidharan S, Hazam PK, Ramakrishnan V. Symmetry-Directed Self-Organization in Peptide Nanoassemblies through Aromatic π-π Interactions. J Phys Chem B 2017; 121:404-411. [PMID: 27935713 DOI: 10.1021/acs.jpcb.6b09474] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Almost all biological systems are assemblies of one or more biomolecules from nano- to macrodimensions. Unlike inorganic molecules, peptide systems attune with the conceptual framework of aggregation models when forming nanoassemblies. Three significant recent theoretical models have indicated that nucleation, end-to-end association, and geometry of growth are determined primarily by the size and electrostatics of the individual basic building blocks. In this study, we tested six model systems, differentially modulating the prominence of three design variables, namely, aromatic π-π interactions, local electrostatics, and overall symmetry of the basic building unit. Our results indicate that the crucial design elements in a peptide-based nanoassembly are (a) a stable extended π-π interaction network, (b) size, and (c) overall symmetry of the basic building blocks. The six model systems represent all of the design variables in the best manner possible, considering the complexity of a biomolecule. The results provide important directives in deciding the morphology and crystallinity of peptide nanoassemblies.
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Affiliation(s)
- Sajitha Sasidharan
- Department of Biosciences & Bioengineering, Indian Institute of Technology Guwahati , Guwahati 781039, India
| | - Prakash Kishore Hazam
- Department of Biosciences & Bioengineering, Indian Institute of Technology Guwahati , Guwahati 781039, India
| | - Vibin Ramakrishnan
- Department of Biosciences & Bioengineering, Indian Institute of Technology Guwahati , Guwahati 781039, India
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Affiliation(s)
- Sungsu Kim
- Department of Mathematics, University of Louisiana, Lafayette, LA, USA
| | - Ashis SenGupta
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, India
- Department of Biostatistics and Epidemiology, Augusta University, Augusta, GA, USA
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Mapping the Geometric Evolution of Protein Folding Motor. PLoS One 2016; 11:e0163993. [PMID: 27716851 PMCID: PMC5055333 DOI: 10.1371/journal.pone.0163993] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022] Open
Abstract
Polypeptide chain has an invariant main-chain and a variant side-chain sequence. How the side-chain sequence determines fold in terms of its chemical constitution has been scrutinized extensively and verified periodically. However, a focussed investigation on the directive effect of side-chain geometry may provide important insights supplementing existing algorithms in mapping the geometrical evolution of protein chains and its structural preferences. Geometrically, folding of protein structure may be envisaged as the evolution of its geometric variables: ϕ, and ψ dihedral angles of polypeptide main-chain directed by χ1, and χ2 of side chain. In this work, protein molecule is metaphorically modelled as a machine with 4 rotors ϕ, ψ, χ1 and χ2, with its evolution to the functional fold is directed by combinations of its rotor directions. We observe that differential rotor motions lead to different secondary structure formations and the combinatorial pattern is unique and consistent for particular secondary structure type. Further, we found that combination of rotor geometries of each amino acid is unique which partly explains how different amino acid sequence combinations have unique structural evolution and functional adaptation. Quantification of these amino acid rotor preferences, resulted in the generation of 3 substitution matrices, which later on plugged in the BLAST tool, for evaluating their efficiency in aligning sequences. We have employed BLOSUM62 and PAM30 as standard for primary evaluation. Generation of substitution matrices is a logical extension of the conceptual framework we attempted to build during the development of this work. Optimization of matrices following the conventional routines and possible application with biologically relevant data sets are beyond the scope of this manuscript, though it is a part of the larger project design.
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Čakić Semenčić M, Kodrin I, Barišić L, Nuskol M, Meden A. Synthesis and Conformational Study of Monosubstituted Aminoferrocene‐Based Peptides Bearing Homo‐ and Heterochiral Pro‐Ala Sequences. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mojca Čakić Semenčić
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Ivan Kodrin
- Department of ChemistryFaculty of ScienceUniversity of ZagrebHorvatovac 102A10000ZagrebCroatia
| | - Lidija Barišić
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Marko Nuskol
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Anton Meden
- Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaVecna pot 1131000LjubljanaSlovenia
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45
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A novel secondary structure based on fused five-membered rings motif. Sci Rep 2016; 6:31483. [PMID: 27511362 PMCID: PMC4980606 DOI: 10.1038/srep31483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/19/2016] [Indexed: 02/03/2023] Open
Abstract
An analysis of protein structures indicates the existence of a novel, fused five-membered rings motif, comprising of two residues (i and i + 1), stabilized by interresidue Ni+1–H∙∙∙Ni and intraresidue Ni+1–H∙∙∙O=Ci+1 hydrogen bonds. Fused-rings geometry is the common thread running through many commonly occurring motifs, such as β-turn, β-bulge, Asx-turn, Ser/Thr-turn, Schellman motif, and points to its structural robustness. A location close to the beginning of a β-strand is rather common for the motif. Devoid of side chain, Gly seems to be a key player in this motif, occurring at i, for which the backbone torsion angles cluster at ~(−90°, −10°) and (70°, 20°). The fused-rings structures, distant from each other in sequence, can hydrogen bond with each other, and the two segments aligned to each other in a parallel fashion, give rise to a novel secondary structure, topi, which is quite common in proteins, distinct from two major secondary structures, α-helix and β-sheet. Majority of the peptide segments making topi are identified as aggregation-prone and the residues tend to be conserved among homologous proteins.
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46
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Genetic variability of VP7, VP4, VP6 and NSP4 genes of common human G1P[8] rotavirus strains circulating in Italy between 2010 and 2014. Virus Res 2016; 220:117-28. [DOI: 10.1016/j.virusres.2016.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/20/2016] [Accepted: 04/20/2016] [Indexed: 12/12/2022]
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47
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Sharma GVM, Anjaiah G, Kanakaraju M, Sudhakar B, Chatterjee D, Kunwar AC. Synthesis of a new β-amino acid with a 3-deoxy-L-ara furnaoside side chain: the influence of the side chain on the conformation of α/β-peptides. Org Biomol Chem 2016; 14:503-515. [PMID: 26489370 DOI: 10.1039/c5ob01753j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The important role of side chains in the stabilization of helical folds in peptidic foldamers containing C-linked carbo-β-amino acids (β-Caa), an interesting class of β-amino acids, with carbohydrate side chains has been extensively elaborated. As a pragmatic approach to alleviate the interference of substituents in the side chains on the folding propensities of the peptides, they are often modified or removed. The present study reports the synthesis of a new β-Caa with a 3-deoxy-L-ara furanoside side chain, [(R)-β-Caa(da)], from D-glucose, and its use in the synthesis of α/β-peptides in 1 : 1 alternation with D-Ala. The synthesis of peptides using (R)-β-Caa(da), was facile unlike those from (R)-β-Caa(a) having the L-ara furanoside side chain. The detailed NMR, molecular dynamics (MD) and CD studies on the new α/β-peptides showed the presence of robust left-handed 11/9-mixed helices. The study demonstrates that the new (R)-β-Caa(da), behaves differently compared to the other two related monomers, (R)-β-Caa(x) with the D-xylo furanoside side chain and (R)-β-Caa(a).
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Affiliation(s)
- Gangavaram V M Sharma
- Organic and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India.
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48
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A multivariate circular distribution with applications to the protein structure prediction problem. J MULTIVARIATE ANAL 2016. [DOI: 10.1016/j.jmva.2015.09.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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49
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Statistical inference for homologous gene pairs between two circular genomes: a new circular–circular regression model. STAT METHOD APPL-GER 2015. [DOI: 10.1007/s10260-015-0341-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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Leader DP, Milner-White EJ. Bridging of partially negative atoms by hydrogen bonds from main-chain NH groups in proteins: The crown motif. Proteins 2015; 83:2067-76. [DOI: 10.1002/prot.24923] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/29/2015] [Accepted: 09/01/2015] [Indexed: 11/05/2022]
Affiliation(s)
- David P. Leader
- College of Medical, Veterinary and Life Sciences, University of Glasgow; Glasgow G12 8QQ United Kingdom
| | - E. James Milner-White
- College of Medical, Veterinary and Life Sciences, University of Glasgow; Glasgow G12 8QQ United Kingdom
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