Type I interferon structures: Possible scaffolds for the interferon-alpha receptor complex

2002 ◽  
Vol 80 (8) ◽  
pp. 1166-1173 ◽  
Author(s):  
Tattanahalli L Nagabhushan ◽  
Paul Reichert ◽  
Mark R Walter ◽  
Nicholas J Murgolo
Keyword(s):  
Structural Model ◽  
Structural Information ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Type I Interferons ◽  
Dimensional Structure ◽  
Type I ◽  
Receptor Complex ◽  
X Ray Crystallography ◽  
Receptor Complexes

The structures of several type I interferons (IFNs) are known. We review the structural information known for IFN alphas and compare them to other interferons and cytokines. We also review the structural information known or proposed for IFN–cell receptor complexes. However, the structure of the IFN – cell receptor – IFN receptor2 (IFNAR2) and IFN receptor1 (IFNAR1) complex has not yet been determined. This paper describes a structural model of human IFN-IFNAR2/IFNAR1 complex using human IFN-α2b dimer as the ligand. Both the structures of recombinant human IFN-α2b and IFN-β were determined by X-ray crystallography as zinc-mediated dimers. Our proposed model was generated using human IFN-α2b dimer docked with IFNAR2/IFNAR1. We compare our model with the receptor complex models proposed for IFN-β and IFN-γ to contrast similarities and differences. The mutual binding sites of human IFN-α2b and IFNAR2/IFNAR1 complex are consistent with available mutagenesis studies.Key words: three dimensional structure, antiviral activity, receptor, interferon.

scholarly journals Structural Model for 12-Helix Transporters Belonging to the Major Facilitator Superfamily

2003 ◽  
Vol 185 (5) ◽  
pp. 1712-1718 ◽  
Author(s):  
Teruhisa Hirai ◽  
Jürgen A. W. Heymann ◽  
Peter C. Maloney ◽  
Sriram Subramaniam
Keyword(s):  
Structural Model ◽  
Structural Information ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Bound State ◽  
Major Facilitator Superfamily ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Major Facilitator ◽  
Related Proteins

ABSTRACT The major facilitator superfamily includes a large collection of evolutionarily related proteins that have been implicated in the transport of a variety of solutes and metabolites across the membranes of organisms ranging from bacteria to humans. We have recently reported the three-dimensional structure, at 6.5 Å resolution, of the oxalate transporter, OxlT, a representative member of this superfamily. In the oxalate-bound state, 12 helices surround a central cavity to form a remarkably symmetrical structure that displays a well-defined pseudo twofold axis perpendicular to the plane of the membrane as well as two less pronounced, mutually perpendicular pseudo twofold axes in the plane of the membrane. Here, we combined this structural information with sequence information from other members of this protein family to arrive at models for the arrangement of helices in this superfamily of transport proteins. Our analysis narrows down the number of helix arrangements from about a billion starting possibilities to a single probable model for the relative spatial arrangement for the 12 helices, consistent both with our structural findings and with the majority of previous biochemical studies on members of this superfamily.

scholarly journals Raman optical activity: A new light on proteins, carbohydrates and glycoproteins

2006 ◽  
Vol 28 (3) ◽  
pp. 27-31 ◽  
Author(s):  
Laurence D. Barron
Keyword(s):  
Structural Biology ◽  
Optical Activity ◽  
Large Range ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
The Novel ◽  
X Ray ◽  
X Ray Crystallography ◽  
Raman Optical Activity

The core techniques of structural biology, namely X-ray crystallography and multidimensional NMR, are often not applicable to many important samples due to fundamental experimental problems, such as the lack of suitable crystals in the X-ray case or excessive size or flexibility for NMR. Carbohydrates and glycoproteins are especially challenging in this respect. The novel technique of vibrational ROA (Raman optical activity), which combines the advantages of vibrational spectroscopy with the extra sensitivity to three-dimensional structure of chiroptical methods such as CD (circular dichroism), has much promise for studying a large range of biomolecules, from the smallest to the largest, in aqueous solution. Among other things, it is capable of providing structural information about both the polypeptide and the carbohydrate structure of intact glycoproteins and should become an indispensable spectroscopy tool for glycobiology.

Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid–binding residues

2020 ◽  
Vol 13 (636) ◽  
pp. eaaz5599 ◽  
Author(s):  
Kelan Chen ◽  
Richard W. Birkinshaw ◽  
Alexandra D. Gurzau ◽  
Iromi Wanigasuriya ◽  
Ruoyun Wang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Muscular Dystrophy ◽  
Three Dimensional ◽  
Underlying Mechanism ◽  
Structural Features ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Dimensional Structure ◽  
Nucleic Acid Binding ◽  
X Ray Crystallography ◽  
Hinge Domain

Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) is an epigenetic regulator in which polymorphisms cause the human developmental disorder, Bosma arhinia micropthalmia syndrome, and the degenerative disease, facioscapulohumeral muscular dystrophy. SMCHD1 is considered a noncanonical SMC family member because its hinge domain is C-terminal, because it homodimerizes rather than heterodimerizes, and because SMCHD1 contains a GHKL-type, rather than an ABC-type ATPase domain at its N terminus. The hinge domain has been previously implicated in chromatin association; however, the underlying mechanism involved and the basis for SMCHD1 homodimerization are unclear. Here, we used x-ray crystallography to solve the three-dimensional structure of the Smchd1 hinge domain. Together with structure-guided mutagenesis, we defined structural features of the hinge domain that participated in homodimerization and nucleic acid binding, and we identified a functional hotspot required for chromatin localization in cells. This structure provides a template for interpreting the mechanism by which patient polymorphisms within the SMCHD1 hinge domain could compromise function and lead to facioscapulohumeral muscular dystrophy.

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

2019 ◽  
Vol 52 (6) ◽  
pp. 1422-1426
Author(s):  
Rajendran Santhosh ◽  
Namrata Bankoti ◽  
Adgonda Malgonnavar Padmashri ◽  
Daliah Michael ◽  
Jeyaraman Jeyakanthan ◽  
...  
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Data Bank ◽  
Protein Crystal ◽  
Dimensional Structure ◽  
Protein Structure Analysis ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Polypeptide Chains

Missing regions in protein crystal structures are those regions that cannot be resolved, mainly owing to poor electron density (if the three-dimensional structure was solved using X-ray crystallography). These missing regions are known to have high B factors and could represent loops with a possibility of being part of an active site of the protein molecule. Thus, they are likely to provide valuable information and play a crucial role in the design of inhibitors and drugs and in protein structure analysis. In view of this, an online database, Missing Regions in Polypeptide Chains (MRPC), has been developed which provides information about the missing regions in protein structures available in the Protein Data Bank. In addition, the new database has an option for users to obtain the above data for non-homologous protein structures (25 and 90%). A user-friendly graphical interface with various options has been incorporated, with a provision to view the three-dimensional structure of the protein along with the missing regions using JSmol. The MRPC database is updated regularly (currently once every three months) and can be accessed freely at the URL http://cluster.physics.iisc.ac.in/mrpc.

Structure and conformation of the hydrochloride of pseudoisocytidine, an antileukemic C-nucleoside

1980 ◽  
Vol 58 (16) ◽  
pp. 1633-1638 ◽  
Author(s):  
George I. Birnabaum ◽  
Kyoichi A. Watanabe ◽  
Jack J. Fox
Keyword(s):  
Heavy Atom ◽  
Three Dimensional ◽  
Direct Methods ◽  
Dimensional Structure ◽  
Side Chain ◽  
Hydrogen Atoms ◽  
Triclinic Space Group ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Sugar Ring

The three-dimensional structure of pseudoisocytidine hydrochloride was determined by X-ray crystallography. The crystals belong to the triclinic space group P1 and the cell dimensions are a = 6.623(2), b = 8.053(2), c = 6.201(2) Å, α = 108.35(2), β = 101.36(2), γ = 93.54(2) °. Intensity data were measured with a diffractometer and the structure was solved by a combination of heavy-atom and direct methods. Least-squares refinement, which included hydrogen atoms, converged at R = 0.040. The conformation about the glycosyl bond is anti (χCC = 21.6°), the pucker of the furanose ring is C(1′)exo, and the conformation of the —CH2OH side chain is gauche–trans (t). An examination of bond lengths indicates that of the three main resonance forms of the isocytosine cation the fully conjugated one contributes more to the structure than the cross-conjugated one. Bond angles in the sugar ring reflect its rare conformation.

The Integrative Establishment of a Three-Dimensional Structure Model of Changling Gas Field in Changling Fault Depression

2014 ◽  
Vol 556-562 ◽  
pp. 3779-3782
Author(s):  
Xiao Yu Yu ◽  
Xue Li ◽  
Xiao Song Li ◽  
Guo Yi Zhang
Keyword(s):  
Structural Model ◽  
High Reliability ◽  
Three Dimensional ◽  
Physical Property ◽  
Modeling Technique ◽  
Dimensional Structure ◽  
Gas Field ◽  
3D Geological Modeling ◽  
Micro Features ◽  
Reservoir Description

The three-dimensional (3D) geological modeling technique which is considered as an important skill of fine reservoir description has been gaining more and more attention. On one hand, it can efficiently promote the transformation of reservoir description from two-dimensional (2D) to 3D, and from qualification to quantification as well. The 3D reservoir geological model can be used as basic geological knowledge in terms of adjusting well patterns and indicating remaining oil distribution, through reflecting the spatial distribution characteristics and the variation of the reservoir physical property. On the other hand, the 3D modeling technique specializes in the representation of local micro features in comparison of regular ways. This article aims at subtly describing the structural modeling of Changling gas field of Changling fault depression. The result of this case study shows that the establishment of structural model is consistent with the understanding of fault development which was proved during the process of producing gas, thus the structural model has high reliability. Therefore, the structural model is of great guiding significance for the design of new well and the well patter optimization.

scholarly journals SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

2020 ◽  
Vol 36 (11) ◽  
pp. 3372-3378
Author(s):  
Alexander Gress ◽  
Olga V Kalinina
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Structural Data ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Precise Measure ◽  
The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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