Mycocypins are cysteine protease inhibitors isolated from the mushrooms Clitocybe nebularis and Macrolepiota procera. The crystal structures of the complex of clitocypin with the papainlike cysteine protease cathepsin V, macrocypin and clitocypin alone have revealed yet another motif of binding to papainlike cysteine proteases. The binding loops present a versatile surface with the potential to bind to additional classes of proteases. When appropriately engineered, they could provide the basis for possible exploitation in crop protection.
COBISS.SI-ID: 23263527
It is more than 50 years since the lysosome was discovered. Since then its hydrolytic machinery, including proteases and other hydrolases, has been fairly well identified and characterized. Among these are the cyste ine cathepsins, members of the family of papainlike cysteine proteases. They have unique reactive site properties and an uneven tissue specific expression pattern. In living organisms their activity is a delicate balance of expression, targeting, zymogen activation, inhibition by protein inhibitors and degradation. The specificity of their substrate binding sites, smallmolecule inhibitor repertoire and crystal structures are providing new tools for research and development. Their unique reactive site properties have made it possible to confine the targets simply by the use of appropriate reactive groups. The epoxysuccinyls still dominate the field, but now nitriles seem to be the most appropriate “warhead”. The view of cysteine cathepsins as lysosomal proteases is changing as there is now clear evidence of their localization in other cellular compartments. Besides being involved in protein turnover, they build an important part of the endosomal antigen presentation machinery. Together with the growing number of nonendosomal roles of cysteine cathepsins is growing also the knowledge of their involvement in diseases, such as cancer and rheumatoid arthritis, among others. Finally, cysteine cathepsins are important regulators and signaling molecules of an unimaginable number of biological processes. The current challenge is to identify their endogenous substrates, in order to gain an insight into the mechanisms of substrate degradation and processing. In this review, some of the remarkable advances that have taken place in the past decade are presented. The article (as well as the whole issue BBA proteins and proteomics vol. 1824/1, 2012) was dedicated to Nobel laureate Christian de Duve.
COBISS.SI-ID: 25347623
Protein inhibitors are tools of nature to control the activity of proteolytic enzymes. They come in different shapes and sizes. The βtrefoil protease inhibitors originate from plants and were first discovered by Kunitz, and later complemented with representatives from higher fungi. They inhibit serine (families S1 and S8) and cysteine proteases (families C1 and C13) as well as other hydrolases. Their versatility is the result of the plasticity of the loops coming out of the stable βtrefoil scaffold. For this reason, they display several different mechanisms of inhibition involving different positions of the loops and their combinations. Natural diversity, as well as the initial successes in de novo protein engineering, makes the β trefoil proteins as a promising starting point for the generation of strong, specific, multitarget inhibitors capable of inhibiting multiple types of hydrolytic enzymes and simultaneously interacting with different protein, carbohydrate, or DNA molecules. This pool of knowledge opens up new possibilities for the exploration of their naturally occurring as well as modified properties for applications in many fields of medicine, biotechnology, and agriculture. This paper was published in a special issue dedicated to 75th anniversary of my mentor Nobel laureate Robert Huber.
COBISS.SI-ID: 26303015
Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map calculation methods. The conclusion is that AK maps can be useful throughout the entire progress of crystal structure determination, offering the possibility of improved map interpretation.
COBISS.SI-ID: 22793511
MAIN is software designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. With MAIN, it is possible to perform density modifications, manual and semi automated or automated model building and rebuilding, real and reciprocal space structure optimization and refinement, map calculations, and various types of molecular structure validation. The prompt availability of various analytical tools and immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed, refined structure. The extraordinary depth perception of molecular objects in 3D that is provided by MAIN is achieved by the clarity and contrast of colors and smooth rotation of the displayed objects. MAIN allows simultaneous work on several molecular models and various crystal forms. The strength of MAIN lies in its manipulation of averaged density maps and molecular models when non-crystallographic symmetry (NCS) is present. With MAIN, it is possible to optimize NCS parameters and envelopes and to refine the structure in single or multiple crystal forms.
COBISS.SI-ID: 26802727