A method for the analysis of domain movements in large biomolecular complexes.

School of Computing Sciences and School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom.
Proteins Structure Function and Bioinformatics (Impact Factor: 2.92). 07/2009; 76(1):201-12. DOI: 10.1002/prot.22339
Source: PubMed

ABSTRACT A new method for the analysis of domain movements in large, multichain, biomolecular complexes is presented. The method is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. The method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA, or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a "rotation space" and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have colocated points. Thus a domain can be identified from the clustering of points from blocks that span it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. Here, we report on the application of the method to biomolecules covering a considerable size range: hemoglobin, liver alcohol dehydrogenase, S-Adenosylhomocysteine hydrolase, aspartate transcarbamylase, and the 70S ribosome. The results provide a depiction of the conformational change within each molecule that is easily understood, giving a perspective that is expected to lead to new insights. Of particular interest is the allosteric mechanism in some of these molecules. Results indicate that common boundaries between subunits and domains are good regions to focus on as movement in one subunit can be transmitted to another subunit through such interfaces.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI–FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5′ flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5′ flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.
    Genes & development 09/2014; 28(28):2276-2290. DOI:10.1101/gad.248492.114 · 12.64 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: RNase J is an essential enzyme in Bacillus subtilis with unusual dual endonuclease and 5'-to-3' exonuclease activities that play an important role in the maturation and degradation of mRNA. RNase J is also a component of the recently identified "degradosome" of B. subtilis. We report the crystal structure of RNase J1 from B. subtilis to 3.0 Å resolution, analysis of which reveals it to be in an open conformation suitable for binding substrate RNA. RNase J is a member of the β-CASP family of zinc-dependent metallo-β-lactamases. We have exploited this similarity in constructing a model for an RNase J1:RNA complex. Analysis of this model reveals candidate-stacking interactions with conserved aromatic side chains, providing a molecular basis for the observed enzyme activity. Comparisons of the B. subtilis RNase J structure with related enzymes reveal key differences that provide insights into conformational changes during catalysis and the role of the C-terminal domain.
    Structure 09/2011; 19(9):1241-51. DOI:10.1016/j.str.2011.06.017 · 6.79 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: As the key component of the musculoskeletal system, the extracellular matrix of soft connective tissues such as ligaments and tendons is a biological example of fibre-reinforced composite but with a complex hierarchical architecture. To establish a comprehensive structure-function relationship at the respective levels (i.e., from molecule to tissue) of the hierarchical architecture is challenging and requires a multidisciplinary approach, involving the integration of findings from the fields of molecular biology, biochemistry, structural biology, materials science and biophysics. Accordingly, in recent years, some of these fields, namely structural biology, materials science and biophysics, have made significant progress in the microscale and nanoscale studies of extracellular matrix using new tools, such as microelectromechanical systems, optical tweezers and atomic force microscopy, complemented by new techniques in simultaneous imaging and mechanical testing and computer modelling. The intent of this paper is to review the key findings on the mechanical response of extracellular matrix at the respective levels of the hierarchical architecture. The main focus is on the structure and function—the findings are compared across the different levels to provide insights that support the goal of establishing a comprehensive structure-function relationship of extracellular matrix. For this purpose, the review is divided into two parts. The first part explores the features of key structural units of extracellular matrix, namely tropocollagen molecule (the lowest level), microfibril, collagen fibril, collagen fibre and fascicle. The second part examines the mechanics of the structural units at the respective levels. Finally a framework for extracellular matrix mechanics is proposed to support the goal to establish a comprehensive structure-function relationship. The framework describes the integration of the mechanisms of reinforcement by the structural units at the respective levels of the hierarchical architecture in a consistent manner, both to allow comparison of these mechanisms, and to make prediction of the interconnection of these mechanisms that can also assist in the identification of effective mechanical pathways. From a design perspective, this is a step in the direction towards the development of effective strategies for engineering materials to replace or repair damaged tissues, and for exogenous cross-linking therapy to enhance the mechanical properties of injured tissues.
    Journal of Biomedical Nanotechnology 10/2014; 10(10):2464-507. DOI:10.1166/jbn.2014.1960 · 7.58 Impact Factor