Architecture of the NS2 protease domain

NS2 is a hydrophobic protein with several putative transmembrane segments. Removal of the N-terminal region containing these segments greatly increased the expression and yield of recombinant NS2 without affecting auto-proteolysis.31'42 The C-terminal domain of NS2 residues 94 to 217 (NS2pro) was expressed in bacteria and purified to homogeneity in the presence of detergents. The crystal structure revealed that NS2pro consists of two subdomains connected by an extended linker (Fig. 5A). The...

A dimeric NS5A reveals potential molecular interaction surfaces

A surface of domain I that was of considerable interest was the buried region between monomers to create the dimeric domain I seen in the crystal structure (Fig. 4). The dimer interface of 678 A2 consists of two patches of buried surface area, one located primarily in subdomain IA, and a second located in subdomain IB. The total buried surface area in the domain I dimer is more than the generally accepted standard of 600 A2 for protein interfaces and has good shape and electrostatic...

Structure and assembly of GAS pili

Pilus structure and assembly in GAS (S. pyogenes) depends on the products of four genes a sortase SrtCl a major pilin subunit which forms the polymeric pilus backbone and two associated minor pilins which decorate the pilus structure. In the Ml strain of GAS these are Spy0129, Spy0128, Spy0125 and Spy0130, respectively.6 The crystal structure of the sortase SrtCl, solved at 2.3 A resolution (H. Kang, unpublished), showed that it has the archetypal sortase fold seen in Staphylococcus aureus...

Potential for a cytoplasmic disulfide bond

Perhaps the most surprising observation from model building and refinement of the structure was the presence of a disulfide bond near the C-terminus of domain I. The disulfide bond connects the sidechains of the conserved Cys 142 and Cys 190, resulting in a covalent link between the loop exiting from p-strand B6 to the C-terminal extension of strand B9 (Fig. 3A). Model refinement without a disulfide at this position placed the sidechains of these cysteine residues in an unfavorable proximity....

EMovie

The 3D structures of macromolecules are difficult to grasp and also to communicate. By their nature, movies or animations are particularly useful for highlighting key features by offering a 'guided tour' of structures and conformation changes. However, high-quality movies are rarely seen because they are currently difficult and time consuming to make. By adopting the traditional movie 'storyboard' concept, which gives guidance and direction to filming, eMovie makes the creation of lengthy...

Entropic contributions to proteinligand interactions

When considering the strength of protein-ligand interactions, not only the energetic contributions but also the entropic components must be taken into account. Entropy S is, as already described, a measure of the order (or disorder) of a system. It allows to estimate over how many degrees of freedom a certain energy content is distributed over the system. One degree of freedom can mean, for example, a certain vibration of the system or a rotation of two single groups around each other. A highly...

Introduction

Type 2 diabetes is a component of a complex metabolic syndrome, characterized by abnormal insulin secretion caused by impaired P-cell function and insulin resistance in target tissues.1,2 It has emerged as one of the world's most debilitating diseases, and its prevalence is reaching epidemic proportions, with over 300 million cases expected worldwide by 2025.3 The patho-genesis of type 2 diabetes is complex and it is influenced by both genetic and environmental factors, including obesity and...

Ribosome mode of action

Ribosomes comprise two ribonucleoprotein subunits (Figure 1a) that associate to form the functional ribosome. While elongation proceeds, each subunit operates cooperatively. The small subunit provides the mRNA binding machinery (Figure 1b) and the path along which the mRNA progresses, the decoding center and the major component controlling translation fidelity. The large subunit performs the main ribosomal catalytic function, namely amino acid polymerization, and provides the protein exit...

Exploring the inhibitor binding site

Fyn Dfg Out

STRUCTURES OF ABL IN COMPLEX WITH DIFFERENT CHEMOTYPES An attractive strategy to overcome or avoid most cases of resistance, would be to administer two drugs in combination, which utilise different binding interactions to inhibit the Abl kinase. In particular, a useful combination could be a compound which binds to the inactive conformation, such as imatinib, with a compound which bound to an active conformation. Examples of chemotypes used as leads for targeting the active conformation...

How large is the contribution of a hydrogen bond to the strength of the proteinligand interaction

Trna Hydrogen Bond

Discussing protein-ligand interactions, the inherent question arises as to how large the contribution of a particular hydrogen bond to the binding affinity actually is. This question may be answered experimentally when two protein-ligand complexes are compared to each other that only differ from one another by one hydrogen bond. Such a comparison is possible, for example, by using protein mutants in which one single amino acid that forms an H-bond to the ligand is replaced by another residue...

Crystal structures molecular modeling and rational design

INITIAL MODELING WORK a-SERIES VERSUS p-SERIES Once the binding mode of both series was established, efforts were started to use the structural information available for the design of structurally novel and diverse inhibitors that would nevertheless retain potency and selectivity. As indicated in Fig. 5, comparison of the binding mode of a- and p-amino acid compounds suggested that the two classes had some shared functionality, in particular the presence of conserved hydrogen bond...

The binding constant Ki describes the strength of the proteinligand interaction

The binding of a ligand to its target protein can be measured. The Binding Constant Ki Eq. 1 may be regarded as a characteristic binding quantity. To be precise, it is a dissociation constant KD, and its reciprocal is the association constant KA. The inhibition constant Ki of enzymes is determined in an assay. Although they do not describe exactly the same, these values are generally used equivalently. In the following only the abbreviation K will be used. The binding constant describes the...