Comparison of the Nucleotide Sequences of Cucumber Mosaic Virus and Brome Mosaic Virus

Cucumber mosaic virus (CMV) and brome mosaic virus (BMV) are isometric plant viruses. Although biologically distinct, they share many common chemical properties. An analysis of the partial genomic RNA sequence available for these two viruses reveals that they are evolutionarily related. Different segments of the genome exhibit different evolutionary rates. The coat proteins, which serve as carriers of genetic material, possess little or no homology. In contrast, the 3a proteins show over 35% homology. The non-coding regions of the genome also exhibit extensive but variable homology suggesting the functional importance of the nucleic acid

Interatomic contacts in viral capsids

Spherical viral capsids possess icosahedral symmetry and are made of a large number of densely- packed protein subunits, each consisting of thousands of atoms. Similarly, a large number of close interactions contribute to packing in crystals of virus particles. A computational method, based on the representation of the three-dimensional shape of the subunits in the icosahedral asymmetric unit as a binary map for the fast evaluation of all short interatomic contacts between subunits within the capsid as well as between particles in the crystal lattice is presented. This method might be useful in the examination of the spatial relations of three-dimensional objects. Its application to sesbania mosaic virus reveals subunit packing dominated by polar interactions, in consistence with observed properties

Contrasting features in the assembly of Sesbania mosaic virus and Physalis mottle virus

Viruses have served as excellent model systems for studies on the assembly/disassembly of macromolecular complexes. We have studied the structures and molecular mechanisms of assembly of two icosahedral ss-RNA plant viruses, Sesbania mosaic virus (SeMV) and Physalis mottle virus (PhMV). The expression of CP gene of these viruses in E. coli was shown to result in the assembly of T=3 virus-like particles (VLPs). In SeMV, the recombinant T=3 particles encapsidate E. coli 23s rRNA and CP mRNA. Deletion of 31 or more amino acids from the N-terminus resulted in the formation of T=1 particles. X-ray diffraction data of three recombinant T=3 capsids and five recombinant T=1 capsids were collected and their structures were solved. A unique structure called b-annulus is found at the icosahedral three-folds of SeMV and many other T=3 viruses. It has been suggested that this structure is essential for T=3 capsid assembly. The structures of recombinant rCP and CP-P53A capsids indicate that despite the differences in the nucleic acid that is encapsidated and the manipulation of the crucial proline at the â-annulus, the core of the CP and the interactions at various interfaces are nearly identical to those of wild type particles. Surprisingly, deletion of residues involved in the formation of b-annulus did not affect capsid assembly. X-ray structural studies have revealed that the b-annulus is indeed absent in these capsids. The structures of T=1 mutants retain accurately several key intersubunit interactions of the native virus. Metal-ion mediated inter-subunit interactions increase the stability of SeMV but are not crucial for the assembly. An arginine rich motif found at the N-terminus of SeMV coat protein has been shown to be essential for RNA encapsidation. These studies have allowed proposition of a plausible model for the assembly of SeMV. The structural, mutational and immunological analysis of PhMV assembly has shown that the N-terminal arm is dynamic and could mediate an early step in the disassembly/assembly of the virus. Several mutants that disrupt interfacial interactions have been generated and their stability and assembly have been investigated. The results show that the coat protein folding and assembly are concerted events in the assembly of PhMV

Crystal and molecular structure of putrescine DL- glutamic acid complex

The polyamines spermine, spermidine, putrescine, cadaverine, etc. have been implicated in a variety of cellular functions. However, details of their mode of interaction with other ubiquitous biomolecules is not known. We have solved a few structures of polyamine-amino acid complexes to understand the nature and mode of their interactions. Here we report the structure of a complex of putrescine with DL-glutamic acid. Comparison of the structure with the structure of putrescine-L-glutamic acid complex reveals the high degree of similarity in the mode of interaction in the two complexes. Despite the presence of a centre of symmetry in the present case, the arrangement of molecules is strikingly similar to the L-glutamic acid complex

Crystal structure of putrescine aspartic acid complex

Polyamines, putrescine, spermidine and spermine are ubiquitous biogenic cations believed to be important for a variety of cellular processes. In order to obtain structural information on the interaction of these amines with other biomolecules, the structure of a complex of putrescine with aspartic acid was determined using single crystal X-ray diffraction methods. The crystals belong monoclinic space group $C_2$ with $a = 21.504 \AA$, $b = 4.779 \AA$, $c = 8.350 \AA$ and $\beta = {97.63}^{\circ}$. The structure was refined to an R factor of 8.4% for 664 reflections. The asymmetric unit contains one aspartic acid and half putrescine molecule. The conformation of aspartic acid corresponds to its most favorable extended structure. The putrescine molecule, although on a 2-fold special position, lacks 2-fold symmetry. The putrescine backbone has a transgauche conformation. The energy required for distorting the putrescine molecule from its most favourable zigzag structure is presumably derived from both hydrogen bonding and electrostatic interactions

Protein structural homology: A metric approach

The flexibility of the polypeptide fold of proteins is essentially due to the rotational freedom about the main chain bonds involving Ca atoms. The polypeptide fold can therefore be represented by virtual bonds joining consecutive Ca atoms. The ordered sequence of virtual torsion and bond angles involving these bonds can be used to specify the fold. Such representations can then be compared to reveal structural similarities using the S. B. Needleman and C. D. Wuensch (1970) algorithm, which has been developed from comparison of amino acid sequences. Such an approach is presented and illustrated with examples. The method is suitable for detecting structural similarities that extend over 7 or more residues

Source and target enzyme signature in serine protease inhibitor active site sequences

Amino acid sequences of proteinaceous proteinase inhibitors have been extensively analysed for deriving information regarding the molecular evolution and functional relationship of these proteins. These sequences have been grouped into several well defined families. It was found that the phylogeny constructed with the sequences corresponding to the exposed loop responsible for inhibition has several branches that resemble those obtained from comparisons using the entire sequence. The major branches of the unrooted tree corresponded to the families to which the inhibitors belonged. Further branching is related to the enzyme specificity of the inhibitor. Examination of the active site loop sequences of trypsin inhibitors revealed that there are strong preferences for specific amino acids at different positions of the loop. These preferences are inhibitor class specific. Inhibitors active against more than one enzyme occur within a class and confirm to class specific sequence in their loops. Hence, only a few positions in the loop seem to determine the specificity. The ability to inhibit the same enzyme by inhibitors that belong to different classes appears to be a result of convergent evolutio

Correlating dynamics to conformational properties:An analysis of atomic displacement parameters (B-values) in high-resolution protein structures

Atomic displacement parameters (ADPs) obtained by high resolution X-ray diffraction studies on single crystals of proteins represent the mean square displacement of atoms about their mean position. The relationship between the flexibility of the protein molecule and its conformation could be examined by a careful analysis of these ADPs. This communication presents the results of such a statistical analysis. It is shown that the ADPs are related to side chain conformations and are low for energetically favourable rotamers. Examination of the dependence of ADPs on non-planar distortions of the peptide geometry as represented by w angle reveals that the parameters depend on the direction of non-planar distortion. Those conformations with w larger than the ideal trans geometry (180°–190°) are more flexible when compared to those with w < 180° (170° 180°). The average ADP of a peptide unit depends weakly on the Ramachandran angles at the corresponding Ca atom. Thus, the flexibility of different segments of the polypeptide appears to be sensitive to the conformation of the side chains as well as the main chain