Three-Dimensional Structure of Aleutian Mink Disease Parvovirus: Implications for Disease Pathogenicity

ABSTRACT The three-dimensional structure of expressed VP2 capsids of Aleutian mink disease parvovirus strain G (ADVG-VP2) has been determined to 22 Å resolution by cryo-electron microscopy and image reconstruction techniques. A structure-based sequence alignment of the VP2 capsid protein of canine parvovirus (CPV) provided a means to construct an atomic model of the ADVG-VP2 capsid. The ADVG-VP2 reconstruction reveals a capsid structure with a mean external radius of 128 Å and several surface features similar to those found in human parvovirus B19 (B19), CPV, feline panleukopenia virus (FPV), and minute virus of mice (MVM). Dimple-like depressions occur at the icosahedral twofold axes, canyon-like regions encircle the fivefold axes, and spike-like protrusions decorate the threefold axes. These spikes are not present in B19, and they are more prominent in ADV compared to the other parvoviruses owing to the presence of loop insertions which create mounds near the threefold axes. Cylindrical channels along the fivefold axes of CPV, FPV, and MVM, which are surrounded by five symmetry-related β-ribbons, are closed in ADVG-VP2 and B19. Immunoreactive peptides made from segments of the ADVG-VP2 capsid protein map to residues in the mound structures. In vitro tissue tropism and in vivo pathogenic properties of ADV map to residues at the threefold axes and to the wall of the dimples.

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NMR three-dimensional structure of the cationic peptide Stigmurin from Tityus stigmurus scorpion venom: In vitro antioxidant and in vivo antibacterial and healing activity

Peptides ◽

10.1016/j.peptides.2020.170478 ◽

2021 ◽

Vol 137 ◽

pp. 170478

Author(s):

Alessandra Daniele-Silva ◽

Suedson de Carvalho Silva Rodrigues ◽

Elizabeth Cristina Gomes dos Santos ◽

Moacir Fernandes de Queiroz Neto ◽

Hugo Alexandre de Oliveira Rocha ◽

...

Keyword(s):

Three Dimensional ◽

Scorpion Venom ◽

Dimensional Structure ◽

Cationic Peptide ◽

Three Dimensional Structure

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In Vivo and In Vitro Studies of Bacillus subtilis Ferrochelatase Mutants Suggest Substrate Channeling in the Heme Biosynthesis Pathway

Journal of Bacteriology ◽

10.1128/jb.184.14.4018-4024.2002 ◽

2002 ◽

Vol 184 (14) ◽

pp. 4018-4024 ◽

Cited By ~ 22

Author(s):

Ulf Olsson ◽

Annika Billberg ◽

Sara Sjövall ◽

Salam Al-Karadaghi ◽

Mats Hansson

Keyword(s):

Bacillus Subtilis ◽

Amino Acid ◽

Three Dimensional ◽

Site Directed Mutagenesis ◽

Dimensional Structure ◽

Amino Acid Residues ◽

Three Dimensional Structure ◽

Activity Measurements

ABSTRACT Ferrochelatase (EC 4.99.1.1) catalyzes the last reaction in the heme biosynthetic pathway. The enzyme was studied in the bacterium Bacillus subtilis, for which the ferrochelatase three-dimensional structure is known. Two conserved amino acid residues, S54 and Q63, were changed to alanine by site-directed mutagenesis in order to detect any function they might have. The effects of these changes were studied in vivo and in vitro. S54 and Q63 are both located at helix α3. The functional group of S54 points out from the enzyme, while Q63 is located in the interior of the structure. None of these residues interact with any other amino acid residues in the ferrochelatase and their function is not understood from the three-dimensional structure. The exchange S54A, but not Q63A, reduced the growth rate of B. subtilis and resulted in the accumulation of coproporphyrin III in the growth medium. This was in contrast to the in vitro activity measurements with the purified enzymes. The ferrochelatase with the exchange S54A was as active as wild-type ferrochelatase, whereas the exchange Q63A caused a 16-fold reduction in V max. The function of Q63 remains unclear, but it is suggested that S54 is involved in substrate reception or delivery of the enzymatic product.

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Folding of the td pre-RNA with the help of the RNA chaperone StpA

Biochemical Society Transactions ◽

10.1042/bst0301175 ◽

2002 ◽

Vol 30 (6) ◽

pp. 1175-1180 ◽

Cited By ~ 11

Author(s):

O. Mayer ◽

C. Waldsich ◽

R. Grossberger ◽

R. Schroeder

Keyword(s):

Conformational Changes ◽

Three Dimensional ◽

Group I Intron ◽

Dimensional Structure ◽

Rna Chaperone ◽

Three Dimensional Structure ◽

Group I ◽

The Impact

The td group I intron is inserted in the reading frame of the thymidylate synthase gene, which is mainly devoid of structural elements. In vivo, translation of the pre-mRNA is required for efficient folding of the intron into its splicing-competent structure. The ribosome probably resolves exon-intron interactions that interfere with splicing. Uncoupling splicing from translation, by introducing a non-sense codon into the upstream exon, reduces the splicing efficiency of the mutant pre-mRNA. Alternatively to the ribosome, co-expression of genes that encode proteins with RNA chaperone activity promote folding of the td pre-mRNA in vivo. These proteins also efficiently accelerate folding of the td pre-mRNA in vitro. In order to understand the mechanism of action of RNA chaperones, we probed the impact of the RNA chaperone StpA on the structure of the td intron in vivo and compared it with that of the well characterized Cyt-18 protein, which is a group-I-intron-specific splicing factor. We found that the two proteins have opposite effects on the structure of the td intron. While StpA loosens the three-dimensional structure, Cyt-18 tightens it up. Furthermore, mutations that destabilize the intron structure render the mutants sensitive to StpA, whereas splicing of these mutants is rescued by Cyt-18. Our results provide direct evidence for protein-induced conformational changes within a catalytic RNA in vivo. Whereas StpA resolves tertiary contacts enabling the RNA to refold, Cyt-18 contributes to the stabilization of the native three-dimensional structure.

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Protein Folding: Search for Basic Physical Models

The Scientific World JOURNAL ◽

10.1100/tsw.2003.50 ◽

2003 ◽

Vol 3 ◽

pp. 623-635 ◽

Cited By ~ 3

Author(s):

Ivan Y. Torshin ◽

Robert W. Harrison

Keyword(s):

Protein Folding ◽

Tertiary Structure ◽

Three Dimensional ◽

Physical Models ◽

Dimensional Structure ◽

Computational Techniques ◽

Linear Sequence ◽

Physical Forces

How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context ofin vivoprotein folding (which has been studied only for a few proteins), the roles of the fundamental physical forces in thein vitrofolding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces). Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

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Putative sequences on Ro60 three-dimensional structure accessible for 4-hydroxy-2-nonenal (HNE) modification compared to in vitro HNE modification of Ro60 sequences

Molecular Immunology ◽

10.1016/j.molimm.2011.12.010 ◽

2012 ◽

Vol 50 (4) ◽

pp. 185-192 ◽

Cited By ~ 3

Author(s):

Biji T. Kurien ◽

Anil D'Souza ◽

Simon Terzyan ◽

R. Hal Scofield

Keyword(s):

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure

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Parvovirus B19 capsid protein VP2 inhibits hematopoiesis in vitro and in vivo: implications for therapeutic use

Experimental Hematology ◽

10.1016/j.exphem.2004.07.016 ◽

2004 ◽

Vol 32 (11) ◽

pp. 1082-1087 ◽

Cited By ~ 6

Author(s):

Oscar Norbeck ◽

Thomas Tolfvenstam ◽

Laurence E. Shields ◽

Magnus Westgren ◽

Kristina Broliden

Keyword(s):

Capsid Protein ◽

Parvovirus B19 ◽

Therapeutic Use

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Invasiveness of human pleural mesothelioma cells is influenced in vitro by the three-dimensional structure of the ECM and its composition

Annals of Anatomy - Anatomischer Anzeiger ◽

10.1016/s0940-9602(02)80072-3 ◽

2002 ◽

Vol 184 (5) ◽

pp. 417-424 ◽

Cited By ~ 5

Author(s):

E.-M. Ehlers ◽

A. Bakhshandeh ◽

G.-J. Wiedemann ◽

W. Kühnel

Keyword(s):

Three Dimensional ◽

Dimensional Structure ◽

Pleural Mesothelioma ◽

Three Dimensional Structure

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Role of YidC in folding of polytopic membrane proteins

The Journal of Cell Biology ◽

10.1083/jcb.200402067 ◽

2004 ◽

Vol 165 (1) ◽

pp. 53-62 ◽

Cited By ~ 143

Author(s):

Shushi Nagamori ◽

Irina N. Smirnova ◽

H. Ronald Kaback

Keyword(s):

Membrane Proteins ◽

Three Dimensional ◽

In Vitro Transcription ◽

Dimensional Structure ◽

Lipid Phase ◽

Lactose Permease ◽

Primary Role ◽

Protein Insertion

YidC of Echerichia coli, a member of the conserved Alb3/Oxa1/YidC family, is postulated to be important for biogenesis of membrane proteins. Here, we use as a model the lactose permease (LacY), a membrane transport protein with a known three-dimensional structure, to determine whether YidC plays a role in polytopic membrane protein insertion and/or folding. Experiments in vivo and with an in vitro transcription/translation/insertion system demonstrate that YidC is not necessary for insertion per se, but plays an important role in folding of LacY. By using the in vitro system and two monoclonal antibodies directed against conformational epitopes, LacY is shown to bind the antibodies poorly in YidC-depleted membranes. Moreover, LacY also folds improperly in proteoliposomes prepared without YidC. However, when the proteoliposomes are supplemented with purified YidC, LacY folds correctly. The results indicate that YidC plays a primary role in folding of LacY into its final tertiary conformation via an interaction that likely occurs transiently during insertion into the lipid phase of the membrane.

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Insights into the molecular basis of sperm–egg recognition in mammals

Reproduction ◽

10.1530/rep.1.00181 ◽

2004 ◽

Vol 127 (4) ◽

pp. 417-422 ◽

Cited By ~ 92

Author(s):

Tanya Hoodbhoy ◽

Jurrien Dean

Keyword(s):

Zona Pellucida ◽

Three Dimensional ◽

Explanatory Models ◽

Dimensional Structure ◽

Side Chain ◽

Egg Recognition ◽

Three Dimensional Structure ◽

Sperm Binding ◽

Single Protein

The zona pellucida surrounding the egg and pre-implantation embryo is required for in vivo fertility and early development. Explanatory models of sperm–egg recognition need to take into account the ability of sperm to bind to ovulated eggs, but not to two-cell embryos. For the last two decades, investigators have sought to identify an individual protein or carbohydrate side chain as the ‘sperm receptor’. However, recent genetic data in mice are more consistent with the three-dimensional structure of the zona pellucida, rather than a single protein (or carbohydrate), determining sperm binding. The mouse and human zonae pellucidae contain three glycoproteins (ZP1, ZP2, ZP3) and, following fertilization, ZP2 is proteolytically cleaved. The replacement of endogenous mouse proteins with human ZP2, ZP3 or both does not alter taxon specificity of sperm binding or prevent fertility. Surprisingly, human ZP2 is not cleaved following fertilization and intact ZP2 correlates with persistent sperm binding to two-cell embryos. Taken together, these data support a model in which the cleavage status of ZP2 modulates the three-dimensional structure of the zona pellucida and determines whether sperm bind (uncleaved) or do not (cleaved).

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