A Carboxylate to Amide Substitution That Switches Protein Folds

An Outlook on the Complexity of Protein Morphogenesis in Health and Disease

The study of the mechanisms whereby proteins achieve their native functionally competent conformation has been a key issue in molecular biosciences over the last 6 decades. Nevertheless, there are several debated issues and open problems concerning some aspects of this fundamental problem. By considering the emerging complexity of the so-called “native state,” we attempt hereby to propose a personal account on some of the key topics in the field, ranging from the relationships between misfolding and diseases to the significance of protein disorder. Finally, we briefly describe the recent and exciting advances in predicting protein structures from their amino acid sequence.

The stability and dynamics of computationally designed proteins

Protein stability, dynamics and function are intricately linked. Accordingly, protein designers leverage dynamics in their designs and gain insight to their successes and failures by analyzing their proteins' dynamics. Molecular dynamics (MD) simulations are a powerful computational tool for quantifying both local and global protein dynamics. This review highlights studies where MD simulations were applied to characterize the stability and dynamics of designed proteins and where dynamics were incorporated into computational protein design. First, we discuss the structural basis underlying the extreme stability and thermostability frequently observed in computationally designed proteins. Next, we discuss examples of designed proteins, where dynamics were not explicitly accounted for in the design process, whose coordinated motions or active site dynamics, as observed by MD simulation, enhanced or detracted from their function. Many protein functions depend on sizeable or subtle conformational changes, so we finally discuss the computational design of proteins to perform a specific function that requires consideration of motion by multi-state design.

Visualizing Protein Folding and Unfolding

Protein folding/unfolding is a complicated process that defies high-resolution characterization by experimental methods. As an alternative, atomistic molecular dynamics simulations are now routinely employed to elucidate and magnify the accompanying conformational changes and the role of solvent in the folding process. However, the level of detail necessary to map the process at high spatial-temporal resolution provides an overwhelming amount of data. As more and better tools are developed for analysis of these large data sets and validation of the simulations, one is still left with the problem of visualizing the results in ways that provide insight into the folding/unfolding process. While viewing and interrogating static crystal structures has become commonplace, more and different approaches are required for dynamic, interconverting, unfolding, and refolding proteins. Here we review a variety of approaches, ranging from straightforward to complex and unintuitive for multiscale analysis and visualization of protein folding and unfolding.

Functional Precision Polymers via Stereo- and Regioselective Polymerization Using Group 6 Metal Alkylidene and Group 6 and 8 Metal Alkylidene N-Heterocyclic Carbene Complexes

The concepts of functional precision polymers and the latest accomplishments in their synthesis are summarized. Synthetic concepts based on chain growth polymerization are compared to iterative synthetic approaches. Here, the term "functional precision polymers" refers to polymers that are not solely hydrocarbon-based but contain functional groups and are characterized by a highly ordered primary structure. If insertion polymerization is used for their synthesis, olefin metathesis-based polymerization techniques, that is, ring-opening metathesis polymerization (ROMP), acyclic diene metathesis (ADMET) polymerization, and the regio- and stereoselective cyclopolymerization of α,ω-diynes are almost exclusively applied. Particularly with regio- and stereospecific ROMP and with cyclopolymerization, the synthesis of tactic polymers and copolymers with high regio-, stereo-, and sequence control can be accomplished; however, it requires carefully tailored transition metal catalysts. The fundamental synthetic concepts and strategies are outlined.