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Meadows J, Röder K. The Effect of Pulling and Twisting Forces on Chameleon Sequence Peptides. Chemphyschem 2023; 24:e202300351. [PMID: 37818741 DOI: 10.1002/cphc.202300351] [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: 05/16/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Chameleon sequences are amino acid sequences found in several distinct configurations in experiment. They challenge our understanding of the link between sequence and structure, and provide insight into structural competition in proteins. Here, we study the energy landscapes for three such sequences, and interrogate how pulling and twisting forces impact the available structural ensembles. Chameleon sequences do not necessarily exhibit multiple structural ensembles on a multifunnel energy landscape when we consider them in isolation. The application of even small forces leads to drastic changes in the energy landscapes. For pulling forces, we observe transitions from helical to extended structures in a very small span of forces. For twisting forces, the picture is much more complex, and highly dependent on the magnitude and handedness of the applied force as well as the reference angle for the twist. Depending on these parameters, more complex and more simplistic energy landscapes are observed alongside more and less diverse structural ensembles. The impact of even small forces is significant, confirming their likely role in folding events. In addition, small forces exerted by the remaining scaffold of a protein may be sufficient to lead to the adoption of a specific structural ensemble by a chameleon sequence.
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Affiliation(s)
- James Meadows
- Department of Chemistry, Durham University, Stockton Road, Durham, DH1 3LE, UK
- Previous affiliation: Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Konstantin Röder
- Randall Centre for Cell & Molecular Biophysics, King's College London, Guy's Campus, Great Maze Pond, London, SE1 1UL, UK
- Previous affiliation: Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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Nakshathram S, Duraisamy R. Protein remote homology recognition using local and global structural sequence alignment. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2022. [DOI: 10.3233/jifs-213522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Protein Remote Homology and fold Recognition (PRHR) is the most crucial task to predict the protein patterns. To achieve this task, Sequence-Order Frequency Matrix-Sampling and Deep learning with Smith-Waterman (SOFM-SDSW) were designed using large-scale Protein Sequences (PSs), which take more time to determine the high-dimensional attributes. Also, it was ineffective since the SW was only applied for local alignment, which cannot find the most matches between the PSs. Hence, in this manuscript, a rapid semi-global alignment algorithm called SOFM-SD-GlobalSW (SOFM-SDGSW) is proposed that facilitates the affine-gap scoring and uses sequence similarity to align the PSs. The major aim of this paper is to enhance the alignment of SW algorithm in both locally and globally for PRHR. In this algorithm, the Maximal Exact Matches (MEMs) are initially obtained by the bit-level parallelism rather than to align the individual characters. After that, a subgroup of MEMs is obtained to determine the global Alignment Score (AS) using the new adaptive programming scheme. Also, the SW local alignment scheme is used to determine the local AS. Then, both local and global ASs are combined to produce a final AS. Further, this resultant AS is considered to train the Support Vector Machine (SVM) classifier to recognize the PRH and folds. Finally, the test results reveal the SOFM-SDGSW algorithm on SCOP 1.53, SCOP 1.67 and Superfamily databases attains an ROC of 0.97, 0.941 and 0.938, respectively, as well as, an ROC50 of 0.819, 0.846 and 0.86, respectively compared to the conventional PRHR algorithms.
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Dong S, Luo S, Huang K, Zhao X, Duan L, Li H. Insights into four helical proteins folding via self-guided Langevin dynamics simulation. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1874558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Shuheng Dong
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Kaifang Huang
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
| | - Hao Li
- School of Physics and Electronics, Shandong Normal University, Jinan, People’s Republic of China
- Department of Science and Technology, Shandong Normal University, Jinan, People’s Republic of China
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McNeill SM, Giles NM, Preston D, Jones PP, Crowley JD, Giles GI. Quadruply Stranded Metallo-Supramolecular Helicate [Pd 2(hextrz) 4] 4+ Acts as a Molecular Mimic of Cytolytic Peptides. Chem Res Toxicol 2020; 33:1822-1834. [PMID: 32347099 DOI: 10.1021/acs.chemrestox.0c00061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Pd2(hextrz)4]4+ is a quadruply stranded helicate, a novel bioinorganic complex designed to mimic the structure and function of proteins due to its high stability and supramolecular size. We have previously reported that [Pd2(hextrz)4]4+ exhibited cytotoxicity toward a range of cell lines, with IC50 values ranging from 3 to 10 μM. Here we demonstrate that [Pd2(hextrz)4]4+ kills cells by forming pores within the cell membrane, a mechanism of cell death analogous to the naturally occurring cytolytic peptides. [Pd2(hextrz)4]4+ induced cell death is characterized by an initial influx of Ca2+, followed by nuclear condensation and mitochondrial swelling. This is accompanied by progressive cell membrane damage that results in the formation of large blebs at the cell surface. This allows the efflux of molecules from the cell leading to loss of cell viability. These data suggest that it may be possible to design metallo-supramolecular complexes to mimic the cytotoxic action of pore forming proteins and peptides and so provide a new class of drug to treat cancer, autoimmune disorders, and microbial infection.
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Affiliation(s)
- Samantha M McNeill
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Niroshini M Giles
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Dan Preston
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Peter P Jones
- Department of Physiology and HeartOtago, University of Otago, Dunedin, New Zealand
| | - James D Crowley
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Gregory I Giles
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. Protein flexibility in the light of structural alphabets. Front Mol Biosci 2015; 2:20. [PMID: 26075209 PMCID: PMC4445325 DOI: 10.3389/fmolb.2015.00020] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/30/2015] [Indexed: 01/01/2023] Open
Abstract
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.
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Affiliation(s)
- Pierrick Craveur
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Agnel P Joseph
- Rutherford Appleton Laboratory, Science and Technology Facilities Council Didcot, UK
| | - Jeremy Esque
- Institut National de la Santé et de la Recherche Médicale U964,7 UMR Centre National de la Recherche Scientifique 7104, IGBMC, Université de Strasbourg Illkirch, France
| | - Tarun J Narwani
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Floriane Noël
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Nicolas Shinada
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Matthieu Goguet
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Sylvain Leonard
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Pierre Poulain
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Ets Poulain Pointe-Noire, Congo
| | - Olivier Bertrand
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Guilhem Faure
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD, USA
| | - Joseph Rebehmed
- Centre National de la Recherche Scientifique UMR7590, Sorbonne Universités, Université Pierre et Marie Curie - MNHN - IRD - IUC Paris, France
| | | | - Lakshmipuram S Swapna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto Toronto, ON, Canada
| | - Ramachandra M Bhaskara
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Department of Theoretical Biophysics, Max Planck Institute of Biophysics Frankfurt, Germany
| | - Jonathan Barnoud
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Laboratoire de Physique, École Normale Supérieure de Lyon, Université de Lyon, Centre National de la Recherche Scientifique UMR 5672 Lyon, France
| | - Stéphane Téletchéa
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Faculté des Sciences et Techniques, Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines, Centre National de la Recherche Scientifique UMR 6286, Université Nantes Nantes, France
| | - Vincent Jallu
- Platelet Unit, Institut National de la Transfusion Sanguine Paris, France
| | - Jiri Cerny
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Catherine Etchebest
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | | | - Jean-Christophe Gelly
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Alexandre G de Brevern
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
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