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Molecules
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Mutations in Compositionally Biased Regions of Proteins
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Mutations in Compositionally Biased Regions of Proteins

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Macromolecular Chemistry".

Deadline for manuscript submissions: closed (15 October 2021) | Viewed by 9813

Special Issue Editors

Dr. Matthew Merski

E-Mail Website
Guest Editor
Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland
Interests: structural biology; protein repeats; x-ray crystallography; protein design
Prof. Dr. Dirk Linke

E-Mail Website
Guest Editor
Department of Biosciences, University of Oslo, 0316 Oslo, Norway
Interests: bacterial adhesion; surface proteins; membrane proteins

Special Issue Information

Dear Colleagues,

Twenty amino acids make up the standard vocabulary of proteins, however many proteins (perhaps even as much as a quarter of all sequences) contain regions in which the alphabet of possible sequences is greatly reduced. This includes protein repeats (oligomeric and domain-sized repeats), poly-amino-acid stretches, low-complexity regions, and coiled coils, but also transmembrane regions. This compositional bias is maintained by a combination of factors (structural, functional, thermodynamic, and genetic) that restrict the free substitutions of amino acids within these protein regions over evolutionary time above and beyond those which exist for non-biased regions. This Special Issue on “Mutations in Compositionally Biased Regions of Proteins” welcomes previously unpublished manuscripts which are primarily focused on studies of amino acid mutations within compositionally biased regions in proteins including but not limited to the enumerated categories. Suitable examples would include structural, functional, or thermodynamic studies of both artificial and natural mutations in these regions, large-scale genetic analyses of natural homologues, and others. We also welcome manuscripts in which the analysis concludes with no obvious effect from the mutations or other apparently inconclusive results.

Dr. Matthew Merski
Prof. Dr. Dirk Linke
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • compositional bias
  • protein repeat
  • low complexity
  • mutation
  • coiled coil
  • poly-aa region
  • transmembrane region
  • inconclusive results

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Published Papers (3 papers)

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Research

20 pages, 11094 KiB  
Article
Sequence and Structure-Based Analyses of Human Ankyrin Repeats
by Broto Chakrabarty and Nita Parekh
Molecules 2022, 27(2), 423; https://doi.org/10.3390/molecules27020423 - 10 Jan 2022
Cited by 4 | Viewed by 3490
Abstract
Ankyrin is one of the most abundant protein repeat families found across all forms of life. It is found in a variety of multi-domain and single domain proteins in humans with diverse number of repeating units. They are observed to occur in several [...] Read more.
Ankyrin is one of the most abundant protein repeat families found across all forms of life. It is found in a variety of multi-domain and single domain proteins in humans with diverse number of repeating units. They are observed to occur in several functionally diverse proteins, such as transcriptional initiators, cell cycle regulators, cytoskeletal organizers, ion transporters, signal transducers, developmental regulators, and toxins, and, consequently, defects in ankyrin repeat proteins have been associated with a number of human diseases. In this study, we have classified the human ankyrin proteins into clusters based on the sequence similarity in their ankyrin repeat domains. We analyzed the amino acid compositional bias and consensus ankyrin motif sequence of the clusters to understand the diversity of the human ankyrin proteins. We carried out network-based structural analysis of human ankyrin proteins across different clusters and showed the association of conserved residues with topologically important residues identified by network centrality measures. The analysis of conserved and structurally important residues helps in understanding their role in structural stability and function of these proteins. In this paper, we also discuss the significance of these conserved residues in disease association across the human ankyrin protein clusters. Full article
(This article belongs to the Special Issue Mutations in Compositionally Biased Regions of Proteins)
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14 pages, 1224 KiB  
Article
Structural Effects of Disease-Related Mutations in Actin-Binding Period 3 of Tropomyosin
by Balaganesh Kuruba, Marta Kaczmarek, Małgorzata Kęsik-Brodacka, Magdalena Fojutowska, Małgorzata Śliwinska, Alla S. Kostyukova and Joanna Moraczewska
Molecules 2021, 26(22), 6980; https://doi.org/10.3390/molecules26226980 - 19 Nov 2021
Cited by 4 | Viewed by 2548
Abstract
Tropomyosin (Tpm) is an actin-binding coiled-coil protein. In muscle, it regulates contractions in a troponin/Ca2+-dependent manner and controls the thin filament lengths at the pointed end. Due to its size and periodic structure, it is difficult to observe small local structural [...] Read more.
Tropomyosin (Tpm) is an actin-binding coiled-coil protein. In muscle, it regulates contractions in a troponin/Ca2+-dependent manner and controls the thin filament lengths at the pointed end. Due to its size and periodic structure, it is difficult to observe small local structural changes in the coiled coil caused by disease-related mutations. In this study, we designed 97-residue peptides, Tpm1.164–154 and Tpm3.1265–155, focusing on the actin-binding period 3 of two muscle isoforms. Using these peptides, we evaluated the effects of cardiomyopathy mutations: I92T and V95A in Tpm1.1, and congenital myopathy mutations R91P and R91C in Tpm3.12. We introduced a cysteine at the N-terminus of each fragment to promote the formation of the coiled-coil structure by disulfide bonds. Dimerization of the designed peptides was confirmed by gel electrophoresis in the presence and absence of dithiothreitol. Using circular dichroism, we showed that all mutations decreased coiled coil stability, with Tpm3.1265–155R91P and Tpm1.164–154I92T having the most drastic effects. Our experiments also indicated that adding the N-terminal cysteine increased coiled coil stability demonstrating that our design can serve as an effective tool in studying the coiled-coil fragments of various proteins. Full article
(This article belongs to the Special Issue Mutations in Compositionally Biased Regions of Proteins)
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15 pages, 901 KiB  
Article
Are Point Mutations in HMG-CoA Reductases (Hmg1 and Hmg2) a Step towards Azole Resistance in Aspergillus fumigatus?
by Irene Gonzalez-Jimenez, Jose Lucio, Alejandra Roldan, Laura Alcazar-Fuoli and Emilia Mellado
Molecules 2021, 26(19), 5975; https://doi.org/10.3390/molecules26195975 - 1 Oct 2021
Cited by 7 | Viewed by 2649
Abstract
Invasive aspergillosis, mainly caused by Aspergillus fumigatus, can lead to severe clinical outcomes in immunocompromised individuals. Antifungal treatment, based on the use of azoles, is crucial to increase survival rates. However, the recent emergence of azole-resistant A. fumigatus isolates is affecting [...] Read more.
Invasive aspergillosis, mainly caused by Aspergillus fumigatus, can lead to severe clinical outcomes in immunocompromised individuals. Antifungal treatment, based on the use of azoles, is crucial to increase survival rates. However, the recent emergence of azole-resistant A. fumigatus isolates is affecting the efficacy of the clinical therapy and lowering the success rate of azole strategies against aspergillosis. Azole resistance mechanisms described to date are mainly associated with mutations in the azole target gene cyp51A that entail structural changes in Cyp51A or overexpression of the gene. However, strains lacking cyp51A modifications but resistant to clinical azoles have recently been detected. Some genes have been proposed as new players in azole resistance. In this study, the gene hmg1, recently related to azole resistance, and its paralogue hmg2 were studied in a collection of fifteen azole-resistant strains without cyp51A modifications. Both genes encode HMG-CoA reductases and are involved in the ergosterol biosynthesis. Several mutations located in the sterol sensing domain (SSD) of Hmg1 (D242Y, G307D/S, P309L, K319Q, Y368H, F390L and I412T) and Hmg2 (I235S, V303A, I312S, I360F and V397C) were detected. The role of these mutations in conferring azole resistance is discussed in this work. Full article
(This article belongs to the Special Issue Mutations in Compositionally Biased Regions of Proteins)
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