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Abraham E, Nitzan A. Molecular chirality quantification: Tools and benchmarks. J Chem Phys 2024; 160:164104. [PMID: 38651805 DOI: 10.1063/5.0200716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
Molecular chirality has traditionally been viewed as a binary property where a molecule is classified as either chiral or achiral, yet in recent decades, mathematical methods for quantifying chirality have been explored. Here, we use toy molecular systems to systematically compare the performance of two state-of-the-art chirality measures: (1) the Continuous Chirality Measure (CCM) and (2) the Chirality Characteristic (χ). We find that both methods exhibit qualitatively similar behavior when applied to simple molecular systems such as a four-site molecule or the polymer double-helix, but we show that the CCM may be more suitable for evaluating the chirality of arbitrary molecules or abstract structures such as normal vibrational modes. We discuss a range of considerations for applying these methods to molecular systems in general, and we provide links to user-friendly codes for both methods. We aim for this paper to serve as a concise resource for scientists attempting to familiarize themselves with these chirality measures or attempting to implement chirality measures in their own work.
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Affiliation(s)
- Ethan Abraham
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Abraham Nitzan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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2
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Mixed chiral and achiral character in substituted ethane: A next generation QTAIM perspective. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sidorova A, Bystrov V, Lutsenko A, Shpigun D, Belova E, Likhachev I. Quantitative Assessment of Chirality of Protein Secondary Structures and Phenylalanine Peptide Nanotubes. NANOMATERIALS 2021; 11:nano11123299. [PMID: 34947648 PMCID: PMC8707344 DOI: 10.3390/nano11123299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 01/25/2023]
Abstract
In this study we consider the features of spatial-structure formation in proteins and their application in bioengineering. Methods for the quantitative assessment of the chirality of regular helical and irregular structures of proteins are presented. The features of self-assembly of phenylalanine (F) into peptide nanotubes (PNT), which form helices of different chirality, are also analyzed. A method is proposed for calculating the magnitude and sign of the chirality of helix-like peptide nanotubes using a sequence of vectors for the dipole moments of individual peptides.
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Affiliation(s)
- Alla Sidorova
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.L.); (D.S.); (E.B.)
- Correspondence:
| | - Vladimir Bystrov
- Institute of Mathematical Problems of Biology, The Branch of Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Russia; (V.B.); (I.L.)
| | - Aleksey Lutsenko
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.L.); (D.S.); (E.B.)
| | - Denis Shpigun
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.L.); (D.S.); (E.B.)
| | - Ekaterina Belova
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.L.); (D.S.); (E.B.)
| | - Ilya Likhachev
- Institute of Mathematical Problems of Biology, The Branch of Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Russia; (V.B.); (I.L.)
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Glycine in Water Favors the Polyproline II State. Biomolecules 2020; 10:biom10081121. [PMID: 32751224 PMCID: PMC7463814 DOI: 10.3390/biom10081121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Conformational preferences of amino acid residues in water are determined by the backbone and side-chain properties. Alanine is known for its high polyproline II (pPII) propensity. The question of relative contributions of the backbone and side chain to the conformational preferences of alanine and other amino acid residues in water is not fully resolved. Because glycine lacks a heavy-atom side chain, glycine-based peptides can be used to examine to which extent the backbone properties affect the conformational space. Here, we use published spectroscopic data for the central glycine residue of cationic triglycine in water to demonstrate that its conformational space is dominated by the pPII state. We assess three commonly used molecular dynamics (MD) force fields with respect to their ability to capture the conformational preferences of the central glycine residue in triglycine. We show that pPII is the mesostate that enables the functional backbone groups of the central residue to form the most hydrogen bonds with water. Our results indicate that the pPII propensity of the central glycine in GGG is comparable to that of alanine in GAG, implying that the water-backbone hydrogen bonding is responsible for the high pPII content of these residues.
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Shalit Y, Tuvi-Arad I. Side chain flexibility and the symmetry of protein homodimers. PLoS One 2020; 15:e0235863. [PMID: 32706779 PMCID: PMC7380632 DOI: 10.1371/journal.pone.0235863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
A comprehensive analysis of crystallographic data of 565 high-resolution protein homodimers comprised of over 250,000 residues suggests that amino acids form two groups that differ in their tendency to distort or symmetrize the structure of protein homodimers. Residues of the first group tend to distort the protein homodimer and generally have long or polar side chains. These include: Lys, Gln, Glu, Arg, Asn, Met, Ser, Thr and Asp. Residues of the second group contribute to protein symmetry and are generally characterized by short or aromatic side chains. These include: Ile, Pro, His, Val, Cys, Leu, Trp, Tyr, Phe, Ala and Gly. The distributions of the continuous symmetry measures of the proteins and the continuous chirality measures of their building blocks highlight the role of side chain geometry and the interplay between entropy and symmetry in dictating the conformational flexibility of proteins.
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Affiliation(s)
- Yaffa Shalit
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
- * E-mail:
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6
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Bonjack M, Avnir D. The near-symmetry of protein oligomers: NMR-derived structures. Sci Rep 2020; 10:8367. [PMID: 32433550 PMCID: PMC7239866 DOI: 10.1038/s41598-020-65097-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry. Despite the many advantages of symmetric packing, protein oligomers are only nearly symmetric, and the origin of this phenomenon is still in need to be fully explored. Here we apply near-symmetry analyses by the Continuous Symmetry Measures methodology of protein homomers to their natural state, namely their structures in solution. NMR-derived structural data serves us for that purpose. We find that symmetry deviations of proteins are by far higher in solution, compared to the crystalline state; that much of the symmetry distortion is due to amino acids along the interface between the subunits; that the distortions are mainly due to hydrophilic amino acids; and that distortive oligomerization processes such as the swap-domain mechanism can be identified by the symmetry analysis. Most of the analyses were carried out on distorted C2-symmetry dimers, but C3 and D2 cases were analyzed as well. Our NMR analysis supports the idea that the crystallographic B-factor represents non-classical crystals, in which different conformers pack in the crystal, perhaps from the conformers which the NMR analysis provides.
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Affiliation(s)
- Maayan Bonjack
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - David Avnir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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James EA, Gillette L, Durinovic-Bello I, Speake C, Bondinas GP, Moustakas AK, Greenbaum CJ, Papadopoulos GK, Kwok WW. DRB4*01:01 Has a Distinct Motif and Presents a Proinsulin Epitope That Is Recognized in Subjects with Type 1 Diabetes. THE JOURNAL OF IMMUNOLOGY 2018; 201:3524-3533. [PMID: 30455401 DOI: 10.4049/jimmunol.1800723] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/15/2018] [Indexed: 11/19/2022]
Abstract
DRB4*01:01 (DRB4) is a secondary HLA-DR product that is part of the high-risk DR4/DQ8 haplotype that is associated with type 1 diabetes (T1D). DRB4 shares considerable homology with HLA-DR4 alleles that predispose to autoimmunity, including DRB1*04:01 and DRB1*04:04. However, the DRB4 protein sequence includes distinct residues that would be expected to alter the characteristics of its binding pockets. To identify high-affinity peptides that are recognized in the context of DRB4, we used an HLA class II tetramer-based approach to identify epitopes within multiple viral Ags. We applied a similar approach to identify antigenic sequences within glutamic acid decarboxylase 65 and pre-proinsulin that are recognized in the context of DRB4. Seven sequences were immunogenic, eliciting high-affinity T cell responses in DRB4+ subjects. DRB1*04:01-restricted responses toward many of these peptides have been previously described, but responses to a novel pre-proinsulin 9-28 peptide were commonly observed in subjects with T1D. Furthermore, T cells that recognized this peptide in the context of DRB4 were present at significantly higher frequencies in patients with T1D than in healthy controls, implicating this as a disease-relevant specificity that may contribute to the breakdown of β cell tolerance in genetically susceptible individuals. We then deduced a DRB4 motif and confirmed its key features through structural modeling. This modeling suggested that the core epitope within the pre-proinsulin 9-28 peptide has a somewhat unusual binding motif, with tryptophan in the fourth binding pocket of DRB4, perhaps influencing the availability of this complex for T cell selection.
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Affiliation(s)
- Eddie A James
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Laurel Gillette
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | | | - Cate Speake
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - George P Bondinas
- Laboratory of Biophysics, Biochemistry, Bioprocessing and Bioproducts, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, GR47100 Arta, Greece
| | - Antonis K Moustakas
- Department of Food Technology, Technological Educational Institute of Ionian Islands, GR27100 Argostoli, Cephalonia, Greece; and
| | - Carla J Greenbaum
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101.,Department of Medicine, University of Washington, Seattle, WA 98195
| | - George K Papadopoulos
- Laboratory of Biophysics, Biochemistry, Bioprocessing and Bioproducts, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, GR47100 Arta, Greece
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101; .,Department of Medicine, University of Washington, Seattle, WA 98195
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Wang H, Avnir D, Tuvi-Arad I. Chiral Ramachandran Plots II: General Trends and Protein Chirality Spectra. Biochemistry 2018; 57:6395-6403. [PMID: 30346734 DOI: 10.1021/acs.biochem.8b00974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The degree of chirality of protein backbone residues is used to enrich the Ramachandran plot (RP) and create three-dimensional chiral RPs with much more structural information. Detailed comparative analysis of the four classical RPs (general, glycine, proline, and pre-proline) is provided, including statistical analysis of quantitative chirality distributions in the maps and in the secondary structures. Our results show that points with outlier chirality levels represent special transitional points in the folded protein such as α-helix kinks, twists of β-strands, and transition points between secondary structures. A protein chirality spectrum in which the degree of chirality of each residue is plotted against the sequence number explores these special points. More than 65000 residues extracted from 200 high-quality proteins are used for this study, which shows that quantitative chirality is a general and useful structural parameter for protein conformational studies.
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Affiliation(s)
- Huan Wang
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Department of Natural Science , The Open University of Israel , Raanana 4353701 , Israel
| | - David Avnir
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel
| | - Inbal Tuvi-Arad
- Department of Natural Science , The Open University of Israel , Raanana 4353701 , Israel
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Carreras A, Bernuz E, Marugan X, Llunell M, Alemany P. Effects of Temperature on the Shape and Symmetry of Molecules and Solids. Chemistry 2018; 25:673-691. [DOI: 10.1002/chem.201801682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/17/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Abel Carreras
- Donostia International Physics Center (DIPC) Paseo Manuel de Lardizabal 4 20018 Donostia, Euskadi Spain
| | - Efrem Bernuz
- Departament de Ciència dels Materials i Química Física andInstitut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona Diagonal 647 08028 Barcelona, Catalunya Spain
| | - Xavier Marugan
- Departament de Ciència dels Materials i Química Física andInstitut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona Diagonal 647 08028 Barcelona, Catalunya Spain
| | - Miquel Llunell
- Departament de Ciència dels Materials i Química Física andInstitut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona Diagonal 647 08028 Barcelona, Catalunya Spain
| | - Pere Alemany
- Departament de Ciència dels Materials i Química Física andInstitut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona Diagonal 647 08028 Barcelona, Catalunya Spain
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