• MeSH
• Biomedical Engineering MeSH
• Macromolecular Substances MeSH
• Molecular Structure MeSH
• Structure-Activity Relationship MeSH

• Conspectus
• Biochemie. Molekulární biologie. Biofyzika
• NML Fields
• biologie
• biomedicínské inženýrství
• biochemie
• NML Publication type
• elektronické časopisy

• MeSH
• Research Support as Topic MeSH
• Gels pharmacology   chemistry   MeSH
• Wound Healing MeSH
• Plasma cytology   MeSH
• Humans MeSH
• Periodontium surgery   pathology   MeSH
• Platelet Count MeSH
• Regeneration physiology   MeSH
• Growth Substances pharmacology   chemistry   classification   MeSH
• Tissue Engineering contraindications   methods   utilization   MeSH
• Check Tag
• Humans MeSH

The NewProt protein engineering portal is a one-stop-shop for in silico protein engineering. It gives access to a large number of servers that compute a wide variety of protein structure characteristics supporting work on the modification of proteins through the introduction of (multiple) point mutations. The results can be inspected through multiple visualizers. The HOPE software is included to indicate mutations with possible undesired side effects. The Hotspot Wizard software is embedded for the design of mutations that modify a proteins' activity, specificity, or stability. The NewProt portal is freely accessible at http://newprot.cmbi.umcn.nl/ and http://newprot.fluidops.net/.

• MeSH
• Databases, Protein * MeSH
• Internet * MeSH
• Models, Molecular MeSH
• Protein Engineering methods   MeSH
• Proteins * chemistry   genetics   metabolism   MeSH
• Software * MeSH
• User-Computer Interface MeSH
• Publication type
• Journal Article MeSH

Protein engineering strategies aimed at constructing enzymes with novel or improved activities, specificities, and stabilities greatly benefit from in silico methods. Computational methods can be principally grouped into three main categories: bioinformatics; molecular modelling; and de novo design. Particularly de novo protein design is experiencing rapid development, resulting in more robust and reliable predictions. A recent trend in the field is to combine several computational approaches in an interactive manner and to complement them with structural analysis and directed evolution. A detailed investigation of designed catalysts provides valuable information on the structural basis of molecular recognition, biochemical catalysis, and natural protein evolution.

• MeSH
• Enzymes genetics   MeSH
• Humans MeSH
• Models, Molecular MeSH
• Mutation MeSH
• Protein Engineering methods   MeSH
• Enzyme Stability MeSH
• Computational Biology methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH

The skin plays a crucial role in protecting the integrity of the body's internal milieu. The loss of this largest organ is incompatible with sustained life. In reconstructive surgery or burn management, substitution of the skin is often necessary. In addition to traditional approaches such as split- or full-thickness skin grafts, tissue flaps and free-tissue transfers, skin bioengineering in vitro or in vivo has been developing over the past decades. It applies the principles and methods of both engineering and life sciences toward the development of substitutes to restore and maintain skin structure and function. Currently, these methods are valuable alternatives or complements to other techniques in reconstructive surgery. This review article deals with the evolution and current approaches to the development of in vitro and in vivo epidermis and dermis.

• MeSH
• Biomedical Engineering MeSH
• Epidermis anatomy & histology   transplantation   MeSH
• Skin Physiological Phenomena MeSH
• Keratinocytes cytology   transplantation   MeSH
• Culture Techniques MeSH
• Skin anatomy & histology   MeSH
• Humans MeSH
• Burns surgery   MeSH
• Skin Transplantation methods   MeSH
• Skin, Artificial * classification   MeSH
• Mouth Mucosa cytology   transplantation   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Review MeSH

Myocardial infarction and ischemic stroke are the most frequent causes of death or disability worldwide. Due to their ability to dissolve blood clots, the thrombolytics are frequently used for their treatment. Improving the effectiveness of thrombolytics for clinical uses is of great interest. The knowledge of the multiple roles of the endogenous thrombolytics and the fibrinolytic system grows continuously. The effects of thrombolytics on the alteration of the nervous system and the regulation of the cell migration offer promising novel uses for treating neurodegenerative disorders or targeting cancer metastasis. However, secondary activities of thrombolytics may lead to life-threatening side-effects such as intracranial bleeding and neurotoxicity. Here we provide a structural biology perspective on various thrombolytic enzymes and their key properties: (i) effectiveness of clot lysis, (ii) affinity and specificity towards fibrin, (iii) biological half-life, (iv) mechanisms of activation/inhibition, and (v) risks of side effects. This information needs to be carefully considered while establishing protein engineering strategies aiming at the development of novel thrombolytics. Current trends and perspectives are discussed, including the screening for novel enzymes and small molecules, the enhancement of fibrin specificity by protein engineering, the suppression of interactions with native receptors, liposomal encapsulation and targeted release, the application of adjuvants, and the development of improved production systems.

• Publication type
• Journal Article MeSH
• Review MeSH

• MeSH
• Biomechanical Phenomena MeSH
• Biomedical Engineering MeSH
• Biotechnology MeSH

• Conspectus
• Biotechnologie. Genetické inženýrství
• NML Fields
• biomedicínské inženýrství

• Keywords
• Biologie molekulární, Proteiny,
• MeSH
• Molecular Biology MeSH
• Proteins MeSH

The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering is the unique dynamism that enables them to exert allosteric control over the catalytic function of enzymes. Thus, when engaging in a transplantation effort, such dynamics in the context of protein structure need consideration. A second practical challenge is identifying successful excision points for the transplantation or grafting. Here, we present LoopGrafter (https://loschmidt.chemi.muni.cz/loopgrafter/), a web server that specifically guides in the loop grafting process between structurally related proteins. The server provides a step-by-step interactive procedure in which the user can successively identify loops in the two input proteins, calculate their geometries, assess their similarities and dynamics, and select a number of loops to be transplanted. All possible different chimeric proteins derived from any existing recombination point are calculated, and 3D models for each of them are constructed and energetically evaluated. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses.

• MeSH
• Internet MeSH
• Models, Molecular MeSH
• Protein Engineering MeSH
• Proteins * genetics   chemistry   MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

The traditional way of rationally engineering enzymes to change their biocatalytic properties utilizes the modifications of their active sites. Another emerging approach is the engineering of structural features involved in the exchange of ligands between buried active sites and the surrounding solvent. However, surprisingly little is known about the effects of mutations that alter the access tunnels on the enzymes' catalytic properties, and how these tunnels should be redesigned to allow fast passage of cognate substrates and products. Thus, we have systematically studied the effects of single-point mutations in a tunnel-lining residue of a haloalkane dehalogenase on the binding kinetics and catalytic conversion of both linear and branched haloalkanes. The hotspot residue Y176 was identified using computer simulations and randomized through saturation mutagenesis, and the resulting variants were screened for shifts in binding rates. Strikingly, opposite effects of the substituted residues on the catalytic efficiency toward linear and branched substrates were observed, which was found to be due to substrate-specific requirements in the critical steps of the respective catalytic cycles. We conclude that not only the catalytic sites, but also the access pathways must be tailored specifically for each individual ligand, which is a new paradigm in protein engineering and de novo protein design. A rational approach is proposed here to address more effectively the task of designing ligand-specific tunnels using computational tools.

• MeSH
• Alkanes chemistry   metabolism   MeSH
• Biocatalysis MeSH
• Hydrocarbons, Halogenated chemistry   metabolism   MeSH
• Hydrolases chemistry   genetics   metabolism   MeSH
• Catalytic Domain genetics   MeSH
• Kinetics MeSH
• Ligands MeSH
• Molecular Structure MeSH
• Mutagenesis, Site-Directed methods   MeSH
• Protein Domains MeSH
• Protein Engineering methods   MeSH
• Molecular Dynamics Simulation MeSH
• Substrate Specificity MeSH
• Protein Binding MeSH
• Binding Sites genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH