1
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Zhao G, Richaud AD, Williamson RT, Feig M, Roche SP. De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS Chem Biol 2024. [PMID: 38916527 DOI: 10.1021/acschembio.4c00236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-H3s) in maximizing antibody-antigen affinity and specificity, the key structural determinants responsible for their adaptability to diverse loop sequences, lengths, and noncanonical structures are hitherto unknown. To address this question, we achieved a de novo synthesis of bulged CDR-H3 mimics excised from their full antibody context. CD and NMR data revealed that these stable standalone β-hairpin scaffolds are well-folded and retain many of the native bulge CDR-H3 features in water. In particular, the tryptophan residue, highly conserved across CDR-H3 sequences, was found to extend the kinked base of these β-bulges through a combination of stabilizing intramolecular hydrogen bond and CH/π interaction. The structural ensemble consistent with our NMR observations exposed the dynamic nature of residues at the base of the loop, suggesting that β-bulges act as molecular hinges connecting the rigid stem to the more flexible loops of CDR-H3s. We anticipate that this deeper structural understanding of CDR-H3s will lay the foundation to inform the design of antibody drugs broadly and engineer novel CDR-H3 peptide scaffolds as therapeutics.
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Affiliation(s)
- Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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2
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Munte CE, Kalbitzer HR. Solution structure and pressure response of thioredoxin-1 of Plasmodium falciparum. PLoS One 2024; 19:e0301579. [PMID: 38635664 PMCID: PMC11025842 DOI: 10.1371/journal.pone.0301579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
We present here the solution structures of the protein thioredoxin-1 from Plasmodium falciparum (PfTrx-1), in its reduced and oxidized forms. They were determined by high-resolution NMR spectroscopy at 293 K on uniformly 13C-, 15N-enriched, matched samples allowing to identification of even small structural differences. PfTrx-1 shows an α/β-fold with a mixed five-stranded β-sheet that is sandwiched between 4 helices in a β1 α1 β2 α2 β3 α3 β4 β5 α4 topology. The redox process of the CGPC motif leads to significant structural changes accompanied by larger chemical shift changes from residue Phe25 to Ile36, Thr70 to Thr74, and Leu88 to Asn91. By high-field high-pressure NMR spectroscopy, rare conformational states can be identified that potentially are functionally important and can be used for targeted drug development. We performed these experiments in the pressure range from 0.1 MPa to 200 MPa. The mean combined, random-coil corrected B1* values of reduced and oxidized thioredoxin are quite similar with -0.145 and -0.114 ppm GPa-1, respectively. The mean combined, random-coil corrected B2* values in the reduced and oxidized form are 0.179 and 0.119 ppm GPa-2, respectively. The mean ratios of the pressure coefficients B2/B1 are -0.484 and -0.831 GPa-1 in the reduced and oxidized form respectively. They differ at some points in the structure after the formation of the disulfide bond between C30 and C33. The thermodynamical description of the pressure dependence of chemical shifts requires the assumption of at least three coexisting conformational states of PfTrx-1. These three conformational states were identified in the reduced as well as in the oxidized form of the protein, therefore, they represent sub-states of the two main oxidation states of PfTrx-1.
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Affiliation(s)
- Claudia Elisabeth Munte
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
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3
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El Khoury G, Azzam W, Rebehmed J. PyProtif: a PyMol plugin to retrieve and visualize protein motifs for structural studies. Amino Acids 2023; 55:1429-1436. [PMID: 37698713 DOI: 10.1007/s00726-023-03323-z] [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: 12/31/2022] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Proteins often possess several motifs and the ones with similar motifs were found to have similar biochemical properties and thus related biological functions. Thereby, multiple databases were developed to store information on such motifs in proteins. For instance, PDBsum stores the results of Promotif's generated structural motifs and Pfam stores pre-computed patterns of functional domains. In addition to the fact that all this stored information is extremely useful, we can further augment its importance if we ought to integrate these motifs into visualization software. In this work, we have developed PyProtif, a plugin for the PyMOL molecular visualization program, which automatically retrieves protein structural and functional motifs from different databases and integrates them in PyMOL for visualization and analyses. Through an expendable menu and a user-friendly interface, the plugin grants the users the ability to study simultaneously multiple proteins and to select and manipulate each motif separately. Thus, this plugin will be of great interest for structural, evolutionary and classification studies of proteins.
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Affiliation(s)
- Gilbert El Khoury
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Wael Azzam
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon.
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4
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de Brevern AG. An agnostic analysis of the human AlphaFold2 proteome using local protein conformations. Biochimie 2023; 207:11-19. [PMID: 36417962 DOI: 10.1016/j.biochi.2022.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/14/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Knowledge of the 3D structure of proteins is a valuable asset for understanding their precise biological mechanisms. However, the cost of production of 3D structures and experimental difficulties limit their obtaining. The proposal of 3D structural models is consequently an appealing alternative. The release of the AlphaFold Deep Learning approach has revolutionized the field. The recent near-complete human proteome proposal makes it possible to analyse large amounts of data and evaluate the results of the approach in greater depth. The 3D human proteome was thus analysed in light of the classic secondary structures, and many less-used protein local conformations (PolyProline II helices, type of γ-turns, of β-turns and of β-bulges, curvature of the helices, and a structural alphabet). Without questioning the global quality of the approach, this analysis highlights certain local conformations, which maybe poorly predicted and they could therefore be better addressed.
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Affiliation(s)
- Alexandre G de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM UMR_S 1134, BIGR, DSIMB Bioinformatics team, F-75014, Paris, France.
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5
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Dhaliwal J, Wagner J. STR-based feature extraction and selection for genetic feature discovery in neurological disease genes. Sci Rep 2023; 13:2480. [PMID: 36774368 PMCID: PMC9922266 DOI: 10.1038/s41598-023-29376-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
Gene expression, often determined by single nucleotide polymorphisms, short repeated sequences known as short tandem repeats (STRs), structural variants, and environmental factors, provides means for an organism to produce gene products necessary to live. Variation in expression levels, sometimes known as enrichment patterns, has been associated with disease progression. Thus, the STR enrichment patterns have recently gained interest as potential genetic markers for disease progression. However, to the best of our knowledge, we are unaware of any study that evaluates and explores STRs, particularly trinucleotide sequences, as machine learning features for classifying neurological disease genes for the purpose of discovering genetic features. Thus, in this paper, we proposed a new metric and a novel feature extraction and selection algorithm based on statistically significant STR-based features and their respective enrichment patterns to create a statistically significant feature set. The proposed new metric has shown that the neurological disease family genes have a non-random AA, AT, TA, TG, and TT enrichment pattern. This is an important result, as it supports prior research that has established that certain trinucleotides, such as AAT, ATA, ATT, TAT, and TTA, are favored during protein misfolding. In contrast, trinucleotides, such as TAA, TAG, and TGA, are favored during premature termination codon mutations as they are stop codons. This suggests that the metric has the potential to identify patterns that may be genetic features in a sample of neurological genes. Moreover, the practical performance and high prediction results of the statistically significant STR-based feature set indicate that variations in STR enrichment patterns can distinguish neurological disease genes. In conclusion, the proposed approach may have the potential to discover differential genetic features for other diseases.
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Affiliation(s)
- Jasbir Dhaliwal
- Faculty of Information Technology, Monash University, Clayton, VIC, 3800, Australia.
| | - John Wagner
- PsychoGenics Inc., Paramus, New Jersey, 07652, United States of America
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6
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Liu H, Kaku CI, Song G, Yuan M, Andrabi R, Burton DR, Walker LM, Wilson IA. Human antibodies to SARS-CoV-2 with a recurring YYDRxG motif retain binding and neutralization to variants of concern including Omicron. Commun Biol 2022; 5:766. [PMID: 35906394 PMCID: PMC9336126 DOI: 10.1038/s42003-022-03700-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 07/11/2022] [Indexed: 01/02/2023] Open
Abstract
Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally identified a YYDRxG motif encoded by IGHD3-22 in CDR H3 that facilitates antibody targeting to a functionally conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences uncovered 100 such antibodies, many of which can neutralize SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to target sarbecoviruses including the Omicron variant. These findings suggest an epitope-targeting strategy to identify potent and broadly neutralizing antibodies for design of pan-sarbecovirus vaccines and antibody therapeutics.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Laura M Walker
- Adimab, LLC, Lebanon, NH, USA. .,Adagio Therapeutics, Inc, Waltham, MA, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. .,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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7
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Mahmoud SS, Al Abrak ES, Aly EM, Fouly MA. Spectroscopic investigation of retinal degeneration unravel molecular changes associated with vision impairment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 266:120459. [PMID: 34634734 DOI: 10.1016/j.saa.2021.120459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Although retinal degeneration is one of the causes of blindness worldwide and involve the loss of the photoreceptors of the retina, the cause(s) of its development still need to be determined in order to reach an effective treatment instead of trying to slow the progression of the disease. Retinal degeneration condition was induced by intravitreal injection of 2 μl of adenosine triphosphate (ATP) solution. The progress of the disease was monitored by retinal imaging (ocular coherence tomography, OCT) after 1, 8 and 15 days of injecting ATP. At the end of each period, retinal tissue was obtained where retinal proteins were extracted and then subjected to spectroscopic studies. Another part of the retinal tissue was investigated by Fourier transform infrared spectroscopy. The OCT images reflect significant reduction in retinal full thickness and provide evidence of intraretinal inflammation while; the obtained results indicate that both primarily and secondary structure of retinal proteins are influenced by the degeneration condition and, the electrical conductance of retinal proteins is decreased due to degeneration condition. Multivariate principal component analysis identifies that the variance noticed in the infrared spectra due to degeneration condition is not time dependent and revealed intra-groups structural dissimilarity. This dissimilarity was clearly resolved by fluorescence study where the content of amino acids phenylalanine, tryptophan and tyrosine varies with the progress of the degeneration condition. All together provide scientific facts that vision impairment is due to loss of signal transduction and formation of protein aggregates as well.
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Affiliation(s)
- Sherif S Mahmoud
- Biophysics and Laser Science Unit, Research Institute of Ophthalmology, Giza, Egypt.
| | - Eman S Al Abrak
- Biophysics and Laser Science Unit, Research Institute of Ophthalmology, Giza, Egypt
| | - Eman M Aly
- Biophysics and Laser Science Unit, Research Institute of Ophthalmology, Giza, Egypt
| | - Marwa A Fouly
- Ophthalmology department, Research Institute of Ophthalmology, Giza, Egypt
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8
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Craveur P, Narwani TJ, Srinivasan N, Gelly JC, Rebehmed J, de Brevern AG. Shaking the β-Bulges. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:14-18. [PMID: 34115590 DOI: 10.1109/tcbb.2021.3088444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
β-bulges are irregularities inside the β-sheets. They represent more than 3 percent of the protein residues, i.e., they are as frequent as 3.10 helices. In terms of evolution, β-bulges are not more conserved than any other local protein conformations within homologous protein structures. In a first of its kind study, we have investigated the dynamical behaviour of β-bulges using the largest known set of protein molecular dynamics simulations. We observed that more than 50 percent of the existing β-bulges in protein crystal structures remained stable during dynamics while more than1/6th were not stable at all and disappeared entirely. Surprisingly, 1.1 percent of β-bulges that appeared remained stable. β-bulges have been categorized in different subtypes. The most common β-bulges' types are the smallest insertion in β-strands (namely AC and AG); they are found as stable as the whole β-bulges dataset. Low occurring types (namely PC and AS), that have the largest insertions, are significantly more stable than expected. Thus, this pioneer study allowed to precisely quantify the stability of the β-bulges, demonstrating their structural robustness, with few unexpected cases raising structural questions.
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9
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Clark RJ, Phan TH, Song A, Ouellette AJ, Conibear AC, Rosengren KJ. A conserved β‐bulge glycine residue facilitates folding and increases stability of the mouse α‐defensin cryptdin‐4. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Richard J. Clark
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
| | - Thanh Huyen Phan
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
| | - Angela Song
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
| | - André J. Ouellette
- Department of Pathology and Laboratory Medicine and USC Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California Los Angeles California USA
| | - Anne C. Conibear
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
| | - K. Johan Rosengren
- The University of Queensland, School of Biomedical Sciences Brisbane Queensland Australia
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10
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Leader DP, Milner-White EJ. The β-link motif in protein architecture. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1040-1049. [PMID: 34342277 DOI: 10.1107/s2059798321006768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/29/2021] [Indexed: 11/10/2022]
Abstract
The β-link is a composite protein motif consisting of a G1β β-bulge and a type II β-turn, and is generally found at the end of two adjacent strands of antiparallel β-sheet. The 1,2-positions of the β-bulge are also the 3,4-positions of the β-turn, with the result that the N-terminal portion of the polypeptide chain is orientated at right angles to the β-sheet. Here, it is reported that the β-link is frequently found in certain protein folds of the SCOPe structural classification at specific locations where it connects a β-sheet to another area of a protein. It is found at locations where it connects one β-sheet to another in the β-sandwich and related structures, and in small (four-, five- or six-stranded) β-barrels, where it connects two β-strands through the polypeptide chain that crosses an open end of the barrel. It is not found in larger (eight-stranded or more) β-barrels that are straightforward β-meanders. In some cases it initiates a connection between a single β-sheet and an α-helix. The β-link also provides a framework for catalysis in serine proteases, where the catalytic serine is part of a conserved β-link, and in cysteine proteases, including Mpro of human SARS-CoV-2, in which two residues of the active site are located in a conserved β-link.
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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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11
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Menard LM, Wood NB, Vigoreaux JO. Secondary Structure of the Novel Myosin Binding Domain WYR and Implications within Myosin Structure. BIOLOGY 2021; 10:603. [PMID: 34209926 PMCID: PMC8301185 DOI: 10.3390/biology10070603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 01/05/2023]
Abstract
Structural changes in the myosin II light meromyosin (LMM) that influence thick filament mechanical properties and muscle function are modulated by LMM-binding proteins. Flightin is an LMM-binding protein indispensable for the function of Drosophila indirect flight muscle (IFM). Flightin has a three-domain structure that includes WYR, a novel 52 aa domain conserved throughout Pancrustacea. In this study, we (i) test the hypothesis that WYR binds the LMM, (ii) characterize the secondary structure of WYR, and (iii) examine the structural impact WYR has on the LMM. Circular dichroism at 260-190 nm reveals a structural profile for WYR and supports an interaction between WYR and LMM. A WYR-LMM interaction is supported by co-sedimentation with a stoichiometry of ~2.4:1. The WYR-LMM interaction results in an overall increased coiled-coil content, while curtailing ɑ helical content. WYR is found to be composed of 15% turns, 31% antiparallel β, and 48% 'other' content. We propose a structural model of WYR consisting of an antiparallel β hairpin between Q92-K114 centered on an ASX or β turn around N102, with a G1 bulge at G117. The Drosophila LMM segment used, V1346-I1941, encompassing conserved skip residues 2-4, is found to possess a traditional helical profile but is interpreted as having <30% helical content by multiple methods of deconvolution. This low helicity may be affiliated with the dynamic behavior of the structure in solution or the inclusion of a known non-helical region in the C-terminus. Our results support the hypothesis that WYR binds the LMM and that this interaction brings about structural changes in the coiled-coil. These studies implicate flightin, via the WYR domain, for distinct shifts in LMM secondary structure that could influence the structural properties and stabilization of the thick filament, scaling to modulation of whole muscle function.
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Affiliation(s)
| | | | - Jim O. Vigoreaux
- Department of Biology, University of Vermont, Burlington, VT 05405, USA; (L.M.M.); (N.B.W.)
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12
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Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. De novo design of transmembrane β barrels. Science 2021; 371:eabc8182. [PMID: 33602829 PMCID: PMC8064278 DOI: 10.1126/science.abc8182] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
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Affiliation(s)
- Anastassia A Vorobieva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sinduja Marx
- Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Q Stiving
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dagan C Marx
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Karen G Fleming
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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13
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Computational analysis of Cyclin D1 gene SNPs and association with breast cancer. Biosci Rep 2021; 41:227573. [PMID: 33438725 PMCID: PMC7846961 DOI: 10.1042/bsr20202269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 01/03/2023] Open
Abstract
CCND1 encodes for Cyclin D1 protein and single-nucleotide polymorphisms (SNPs) can modulate its activity. In the present study, the impact of CCND1 SNPs on structure and/or function of Cyclin D1 protein using in silico tools was investigated. Our analysis revealed only one splice site SNP (c.1988+5G<A) can effect CCND1 function. Subsequently, 78 out of 169 missense variants were predicted as pathogenic by Polyphen2, SIFT, PROVEAN, SNPs&GO, and PANTHER, and 4/78 missense SNPs were further evaluated because these four SNPs were found to be reside in highly conserved region of Cyclin D1. However, they did not show any major impact on tertiary structure and domain of Cyclin D1 but overall R15S and A190S has displayed a significant diseased phenotype and an altered molecular mechanism predicted by MutPred, FATHMM, SNPeffect, SNAP2, and PredictSNP. Consistently, A190S, R179L, and R15S may also cause a decrease in stability of Cyclin D1 anticipated by I-Mutant, HOPE and SNP effect. Furthermore, the Kaplan–Meier plotter has explained that high expression of CCND1 is associated with less survival rate of breast cancer patients. Altogether our study suggests that c.1988+5G<A, R15S, R179L, and A190S SNPs could directly or indirectly destabilize Cyclin D1.
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14
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Leader DP, Milner-White EJ. Identification and characterization of two classes of G1 β-bulge. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:217-223. [PMID: 33559610 PMCID: PMC7869896 DOI: 10.1107/s2059798320015533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022]
Abstract
In standard β-bulges, a residue in one strand of a β-sheet forms hydrogen bonds to two successive residues (`1' and `2') of a second strand. Two categories, `classic' and `G1' β-bulges, are distinguished by their dihedral angles: 1,2-αRβR (classic) or 1,2-αLβR (G1). It had previously been observed that G1 β-bulges are most often found as components of two quite distinct composite structures, suggesting that a basis for further differentiation might exist. Here, it is shown that two subtypes of G1 β-bulges, G1α and G1β, may be distinguished by their conformation (αR or βR) at residue `0' of the second strand. β-Bulges that are constituents of the composite structure named the β-bulge loop are of the G1α type, whereas those that are constituents of the composite structure named β-link here are of the G1β type. A small proportion of G1β β-bulges, but not G1α β-bulges, occur in other contexts. There are distinctive differences in amino-acid composition and sequence pattern between these two types of G1 β-bulge which may have practical application in protein design.
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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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15
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de Brevern AG. Impact of protein dynamics on secondary structure prediction. Biochimie 2020; 179:14-22. [PMID: 32946990 DOI: 10.1016/j.biochi.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 02/08/2023]
Abstract
Protein 3D structures support their biological functions. As the number of protein structures is negligible in regards to the number of available protein sequences, prediction methodologies relying only on protein sequences are essential tools. In this field, protein secondary structure prediction (PSSPs) is a mature area, and is considered to have reached a plateau. Nonetheless, proteins are highly dynamical macromolecules, a property that could impact the PSSP methods. Indeed, in a previous study, the stability of local protein conformations was evaluated demonstrating that some regions easily changed to another type of secondary structure. The protein sequences of this dataset were used by PSSPs and their results compared to molecular dynamics to investigate their potential impact on the quality of the secondary structure prediction. Interestingly, a direct link is observed between the quality of the prediction and the stability of the assignment to the secondary structure state. The more stable a local protein conformation is, the better the prediction will be. The secondary structure assignment not taken from the crystallized structures but from the conformations observed during the dynamics slightly increase the quality of the secondary structure prediction. These results show that evaluation of PSSPs can be done differently, but also that the notion of dynamics can be included in development of PSSPs and other approaches such as de novo approaches.
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Affiliation(s)
- Alexandre G de Brevern
- Biologie Intégrée Du Globule Rouge UMR_S1134, Inserm, Université de Paris, Univ. de la Réunion, Univ. des Antilles, F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France; Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France; IBL, F-75015, Paris, France.
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16
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Narwani TJ, Etchebest C, Craveur P, Léonard S, Rebehmed J, Srinivasan N, Bornot A, Gelly JC, de Brevern AG. In silico prediction of protein flexibility with local structure approach. Biochimie 2019; 165:150-155. [PMID: 31377194 DOI: 10.1016/j.biochi.2019.07.025] [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: 02/28/2018] [Accepted: 07/26/2019] [Indexed: 12/30/2022]
Abstract
Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein's inner flexibility and predicts them as rigid or flexible. PredyFlexy stands differently from other approaches as it relies on the definition of protein flexibility (i) not only taken from crystallographic data, but also (ii) from Root Mean Square Fluctuation (RMSFs) observed in Molecular Dynamics simulations. It also uses a specific representation of protein structures, named Long Structural Prototypes (LSPs). From Position-Specific Scoring Matrix, the 120 LSPs are predicted with a good accuracy and directly used to predict (i) the protein flexibility in three categories (flexible, intermediate and rigid), (ii) the normalized B-factors, (iii) the normalized RMSFs, and (iv) a confidence index. Prediction accuracy among these three classes is equivalent to the best two class prediction methods, while the normalized B-factors and normalized RMSFs have a good correlation with experimental and in silico values. Thus, PredyFlexy is a unique approach, which is of major utility for the scientific community. It support parallelization features and can be run on a local cluster using multiple cores.
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Affiliation(s)
- Tarun J Narwani
- INSERM, U 1134, DSIMB, Univ Paris, Univ de La Réunion, Univ des Antilles, F-75739, Paris, France; Institut National de La Transfusion Sanguine (INTS), F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France
| | - Catherine Etchebest
- INSERM, U 1134, DSIMB, Univ Paris, Univ de La Réunion, Univ des Antilles, F-75739, Paris, France; Institut National de La Transfusion Sanguine (INTS), F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France
| | - Pierrick Craveur
- INSERM, U 1134, DSIMB, Univ Paris, Univ de La Réunion, Univ des Antilles, F-75739, Paris, France; Institut National de La Transfusion Sanguine (INTS), F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France; Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sylvain Léonard
- INSERM, U 1134, DSIMB, Univ Paris, Univ de La Réunion, Univ des Antilles, F-75739, Paris, France; Institut National de La Transfusion Sanguine (INTS), F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France
| | - Joseph Rebehmed
- INSERM, U 1134, DSIMB, Univ Paris, Univ de La Réunion, Univ des Antilles, F-75739, Paris, France; Institut National de La Transfusion Sanguine (INTS), F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France; Department of Computer Science and Mathematics, Lebanese American University, Byblos 1h401 2010, Lebanon
| | | | - Aurélie Bornot
- INSERM, U 1134, DSIMB, Univ Paris, Univ de La Réunion, Univ des Antilles, F-75739, Paris, France; Institut National de La Transfusion Sanguine (INTS), F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France
| | - Jean-Christophe Gelly
- INSERM, U 1134, DSIMB, Univ Paris, Univ de La Réunion, Univ des Antilles, F-75739, Paris, France; Institut National de La Transfusion Sanguine (INTS), F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, Univ Paris, Univ de La Réunion, Univ des Antilles, F-75739, Paris, France; Institut National de La Transfusion Sanguine (INTS), F-75739, Paris, France; Laboratoire D'Excellence GR-Ex, F-75739, Paris, France; Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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17
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Narwani TJ, Craveur P, Shinada NK, Floch A, Santuz H, Vattekatte AM, Srinivasan N, Rebehmed J, Gelly JC, Etchebest C, de Brevern AG. Discrete analyses of protein dynamics. J Biomol Struct Dyn 2019; 38:2988-3002. [PMID: 31361191 DOI: 10.1080/07391102.2019.1650112] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein structures are highly dynamic macromolecules. This dynamics is often analysed through experimental and/or computational methods only for an isolated or a limited number of proteins. Here, we explore large-scale protein dynamics simulation to observe dynamics of local protein conformations using different perspectives. We analysed molecular dynamics to investigate protein flexibility locally, using classical approaches such as RMSf, solvent accessibility, but also innovative approaches such as local entropy. First, we focussed on classical secondary structures and analysed specifically how β-strand, β-turns, and bends evolve during molecular simulations. We underlined interesting specific bias between β-turns and bends, which are considered as the same category, while their dynamics show differences. Second, we used a structural alphabet that is able to approximate every part of the protein structures conformations, namely protein blocks (PBs) to analyse (i) how each initial local protein conformations evolve during dynamics and (ii) if some exchange can exist among these PBs. Interestingly, the results are largely complex than simple regular/rigid and coil/flexible exchange. AbbreviationsNeqnumber of equivalentPBProtein BlocksPDBProtein DataBankRMSfroot mean square fluctuationsCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tarun Jairaj Narwani
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Pierrick Craveur
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nicolas K Shinada
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Discngine, SAS, Paris, France
| | - Aline Floch
- Laboratoire D'Excellence GR-Ex, Paris, France.,Etablissement Français du Sang Ile de France, Créteil, France.,IMRB - INSERM U955 Team 2 « Transfusion et Maladies du Globule Rouge », Paris Est- Créteil Univ, Créteil, France.,UPEC, Université Paris Est-Créteil, Créteil, France
| | - Hubert Santuz
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Akhila Melarkode Vattekatte
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France
| | | | - Joseph Rebehmed
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon
| | - Jean-Christophe Gelly
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France.,IBL, Paris, France
| | - Catherine Etchebest
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France
| | - Alexandre G de Brevern
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France.,IBL, Paris, France
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18
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Craveur P, Narwani TJ, Rebehmed J, de Brevern AG. Investigation of the impact of PTMs on the protein backbone conformation. Amino Acids 2019; 51:1065-1079. [DOI: 10.1007/s00726-019-02747-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/18/2019] [Indexed: 12/17/2022]
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19
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Olajos G, Hetényi A, Wéber E, Szögi T, Fülöp L, Martinek TA. Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches. Org Biomol Chem 2019; 16:5492-5499. [PMID: 30024580 DOI: 10.1039/c8ob01322e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Engineering water-soluble stand-alone β-sandwich mimetics is a current challenge because of the difficulties associated with tailoring long-range interactions. In this work, single cis-(1R,2S)-2-aminocyclohexanecarboxylic acid mutations were introduced into the edge strands of the eight-stranded β-sandwich mimetic structures from the betabellin family. Temperature-dependent NMR and CD measurements, together with thermodynamic analyses, demonstrated that the modified peripheral strands exhibited an irregular and partially disordered structure but were able to exert sufficient shielding on the hydrophobic core to retain the predominantly β-sandwich structure. Although the frustrated interactions decreased the free energy of unfolding, the temperature of the maximum stabilities increased to or remained at physiologically relevant temperatures. We found that the irregular peripheral strands were able to prevent edge-to-edge association and fibril formation in the aggregation-prone model. These findings establish a β-sandwich stabilization and aggregation inhibition approach, which does not interfere with the pillars of the peptide bond or change the net charge of the peptide.
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Affiliation(s)
- Gábor Olajos
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Edit Wéber
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary.
| | - Titanilla Szögi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Tamás A Martinek
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
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20
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Collu F, Spiga E, Chakroun N, Rezaei H, Fraternali F. Probing the early stages of prion protein (PrP) aggregation with atomistic molecular dynamics simulations. Chem Commun (Camb) 2018; 54:8007-8010. [PMID: 29967919 DOI: 10.1039/c8cc04089c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prions are self-replicating infectious proteinaceous agents whose conformations are capable of forming amyloid-like aggregate fibrils. Here we present molecular dynamics simulations aimed at investigating the aggregation process of the β-rich H2H3 domain of the ovine prion protein (H2H3-OvPrPSc), known to be the portion of prion protein carrying oligomerization activity.
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Affiliation(s)
- Francesca Collu
- King's College London, Randall Centre for Cell & Molecular Biophysics, London, UK.
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21
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Sandí MJ, Marshall CB, Balan M, Coyaud É, Zhou M, Monson DM, Ishiyama N, Chandrakumar AA, La Rose J, Couzens AL, Gingras AC, Raught B, Xu W, Ikura M, Morrison DK, Rottapel R. MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity. Sci Signal 2017; 10:10/503/eaan3286. [PMID: 29089450 DOI: 10.1126/scisignal.aan3286] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The PAR-1-MARK pathway controls cell polarity through the phosphorylation of microtubule-associated proteins. Rho-Rac guanine nucleotide exchange factor 2 (ARHGEF2), which activates Ras homolog family member A (RHOA), is anchored to the microtubule network and sequestered in an inhibited state through binding to dynein light chain Tctex-1 type 1 (DYNLT1). We showed in mammalian cells that liver kinase B1 (LKB1) activated the microtubule affinity-regulating kinase 3 (MARK3), which in turn phosphorylated ARHGEF2 at Ser151 This modification disrupted the interaction between ARHGEF2 and DYNLT1 by generating a 14-3-3 binding site in ARHGEF2, thus causing ARHGEF2 to dissociate from microtubules. Phosphorylation of ARHGEF2 by MARK3 stimulated RHOA activation and the formation of stress fibers and focal adhesions, and was required for organized cellular architecture in three-dimensional culture. Protein phosphatase 2A (PP2A) dephosphorylated Ser151 in ARHGEF2 to restore the inhibited state. Thus, we have identified a regulatory switch controlled by MARK3 that couples microtubules to the actin cytoskeleton to establish epithelial cell polarity through ARHGEF2.
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Affiliation(s)
- María-José Sandí
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Marc Balan
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Ming Zhou
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Daniel M Monson
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Arun A Chandrakumar
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - José La Rose
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada
| | - Amber L Couzens
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Deborah K Morrison
- Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - Robert Rottapel
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Princess Margaret Cancer Research Tower, Toronto, Ontario M5G 1L7, Canada. .,Department of Medical Biophysics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Division of Rheumatology, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
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22
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Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GVT, Guan R, Silva DA, Dou J, Pereira JH, Xiao R, Sankaran B, Zwart PH, Montelione GT, Baker D. Principles for designing proteins with cavities formed by curved β sheets. Science 2017; 355:201-206. [PMID: 28082595 PMCID: PMC5588894 DOI: 10.1126/science.aah7389] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/02/2016] [Indexed: 12/23/2022]
Abstract
Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling β-sheet curvature by studying the geometry of β sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved β sheets topped with α helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that β-sheet curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.
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Affiliation(s)
- Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Benjamin Basanta
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Tamuka M Chidyausiku
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Yuefeng Tang
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Gustav Oberdorfer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria
| | - Gaohua Liu
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - G V T Swapna
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rongjin Guan
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jiayi Dou
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Jose Henrique Pereira
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | | | - Peter H Zwart
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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23
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The origin of β-strand bending in globular proteins. BMC STRUCTURAL BIOLOGY 2015; 15:21. [PMID: 26492857 PMCID: PMC4618951 DOI: 10.1186/s12900-015-0048-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/06/2015] [Indexed: 11/10/2022]
Abstract
Background Many β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from that for the twist. We, therefore, investigated the physical origin(s) of β-strand bends. Methods We calculated rotation, twist and bend angles for a four-residue short frame. Fixed-length fragments consisting of six residues found in three consecutive short frames were used to evaluate the twist and bend angles of full-length β-strands. Results We calculated and statistically analyzed the twist and bend angles of β-strands found in globular proteins with known three-dimensional structures. The results show that full-length β-strand bend angles are related to the nearby aromatic residue content, whereas local bend angles are related to the nearby aliphatic residue content. Furthermore, it appears that β-strands bend to maximize their hydrophobic contacts with an abutting hydrophobic surface or to form a hydrophobic side-chain cluster when an abutting hydrophobic surface is absent. Conclusions We conclude that the dominant driving force for full-length β-strand bends is the hydrophobic interaction involving aromatic residues, whereas that for local β-strand bends is the hydrophobic interaction involving aliphatic residues. Electronic supplementary material The online version of this article (doi:10.1186/s12900-015-0048-y) contains supplementary material, which is available to authorized users.
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Buchko GW, Abendroth J, Clifton MC, Robinson H, Zhang Y, Hewitt SN, Staker BL, Edwards TE, Van Voorhis WC, Myler PJ. Structure of a CutA1 divalent-cation tolerance protein from Cryptosporidium parvum, the protozoal parasite responsible for cryptosporidiosis. Acta Crystallogr F Struct Biol Commun 2015; 71:522-30. [PMID: 25945704 PMCID: PMC4427160 DOI: 10.1107/s2053230x14028210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/29/2014] [Indexed: 11/11/2022] Open
Abstract
Cryptosporidiosis is an infectious disease caused by protozoan parasites of the Cryptosporidium genus. Infection is associated with mild to severe diarrhea that usually resolves spontaneously in healthy human adults, but may lead to severe complications in young children and in immunocompromised patients. The genome of C. parvum contains a gene, CUTA_CRYPI, that may play a role in regulating the intracellular concentration of copper, which is a toxic element in excess. Here, the crystal structure of this CutA1 protein, Cp-CutA1, is reported at 2.0 Å resolution. As observed for other CutA1 structures, the 117-residue protein is a trimer with a core ferrodoxin-like fold. Circular dichroism spectroscopy shows little, in any, unfolding of Cp-CutA1 up to 353 K. This robustness is corroborated by (1)H-(15)N HSQC spectra at 333 K, which are characteristic of a folded protein, suggesting that NMR spectroscopy may be a useful tool to further probe the function of the CutA1 proteins. While robust, Cp-CutA1 is not as stable as the homologous protein from a hyperthermophile, perhaps owing to a wide β-bulge in β2 that protrudes Pro48 and Ser49 outside the β-sheet.
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Affiliation(s)
- Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Howard Robinson
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Yanfeng Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Stephen N. Hewitt
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, Washington, USA
- Department of Medical Education and Biomedical Informatics and Department of Global Health, University of Washington, Seattle, Washington, USA
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Andreani J, Söding J. bbcontacts: prediction of β-strand pairing from direct coupling patterns. ACTA ACUST UNITED AC 2015; 31:1729-37. [PMID: 25618863 DOI: 10.1093/bioinformatics/btv041] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/17/2015] [Indexed: 01/08/2023]
Abstract
MOTIVATION It has recently become possible to build reliable de novo models of proteins if a multiple sequence alignment (MSA) of at least 1000 homologous sequences can be built. Methods of global statistical network analysis can explain the observed correlations between columns in the MSA by a small set of directly coupled pairs of columns. Strong couplings are indicative of residue-residue contacts, and from the predicted contacts a structure can be computed. Here, we exploit the structural regularity of paired β-strands that leads to characteristic patterns in the noisy matrices of couplings. The β-β contacts should be detected more reliably than single contacts, reducing the required number of sequences in the MSAs. RESULTS bbcontacts predicts β-β contacts by detecting these characteristic patterns in the 2D map of coupling scores using two hidden Markov models (HMMs), one for parallel and one for antiparallel contacts. β-bulges are modelled as indel states. In contrast to existing methods, bbcontacts uses predicted instead of true secondary structure. On a standard set of 916 test proteins, 34% of which have MSAs with < 1000 sequences, bbcontacts achieves 50% precision for contacting β-β residue pairs at 50% recall using predicted secondary structure and 64% precision at 64% recall using true secondary structure, while existing tools achieve around 45% precision at 45% recall using true secondary structure. AVAILABILITY AND IMPLEMENTATION bbcontacts is open source software (GNU Affero GPL v3) available at https://bitbucket.org/soedinglab/bbcontacts .
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Affiliation(s)
- Jessica Andreani
- Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Johannes Söding
- Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany and Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Zacharias J, Knapp EW. Protein secondary structure classification revisited: processing DSSP information with PSSC. J Chem Inf Model 2014; 54:2166-79. [PMID: 24866861 DOI: 10.1021/ci5000856] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A first step toward three-dimensional protein structure description is the characterization of secondary structure. The most widely used program for secondary structure assignment remains DSSP, introduced in 1983, with currently more than 400 citations per year. DSSP output is in a one-letter representation, where much of the information on DSSP's internal description is lost. Recently it became evident that DSSP overlooks most π-helical structures, which are more prevalent and important than anticipated before. We introduce an alternative concept, representing the internal structure characterization of DSSP as an eight-character string that is human-interpretable and easy to parse by software. We demonstrate how our protein secondary structure characterization (PSSC) code allows for inspection of complicated structural features. It recognizes ten times more π-helical residues than does the standard DSSP. The plausibility of introduced changes in interpreting DSSP information is demonstrated by better clustering of secondary structures in (φ, ψ) dihedral angle space. With a sliding sequence window (SSW), helical assignments with PSSC remain invariant compared with an assignment based on the complete structure. In contrast, assignment with DSSP can be changed by residues in the neighborhood that are in fact not interacting with the residue under consideration. We demonstrate how one can easily define new secondary structure classification schemes with PSSC and perform the classifications. Our approach works without changing the DSSP source code and allows for more detailed protein characterization.
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Affiliation(s)
- Jan Zacharias
- Fachbereich Biologie, Chemie, Pharmazie/Institute of Chemistry and Biochemistry, Freie Universität Berlin , Fabeckstrasse 36A, 14195 Berlin, Germany
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