Molecular dynamics study of interaction and substrate channeling between neuron-specific enolase and B-type phosphoglycerate mutase

Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease

Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure-function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.

Substrate-to-Product Conversion Facilitates Active Site Loop Opening in Yeast Enolase: A Molecular Dynamics Study

Yeast enolase serves as a prototype for metalloenzymes with labile, catalytic active site metal ions and is important for glycolysis and fermentation processes. Herein, microsecond molecular dynamics simulations of the protein-substrate and protein-product complexes are conducted to elucidate the mechanism of the opening of catalytically important active site loops. These simulations indicate that conversion of substrate to product is accompanied by diminished metal coordination and hydrogen-bonding interactions, as well as enhanced loop flexibility. Moreover, free energy simulations show that the loop opening is endergonic when substrate is bound but exergonic when product is bound. Thus, the conversion to product weakens the association of the loop with the ligand and binding site, thereby facilitating the loop opening after catalysis and enabling product release. These insights about active site loop motions in enzyme catalysis may be useful in guiding enzyme design efforts.

Developmental strategies and regulation of cell-free enzyme system for ethanol production: a molecular prospective

Most biomanufacturing systems developed for the production of biocommodities are based on whole-cell systems. However, with the advent of innovative technologies, the focus has shifted from whole-cell towards cell-free enzyme system. Since more than a century, researchers are using the cell-free extract containing the required enzymes and their respective cofactors in order to study the fundamental aspects of biological systems, particularly fermentation. Although yeast cell-free enzyme system is known since long ago, it is rarely been studied and characterized in detail. In this review, we hope to describe the major pitfalls encountered by whole-cell system and introduce possible solutions to them using cell-free enzyme systems. We have discussed the glycolytic and fermentative pathways and their regulation at both transcription and translational levels. Moreover, several strategies employed for development of cell-free enzyme system have been described with their potential merits and shortcomings associated with these developmental approaches. We also described in detail the various developmental approaches of synthetic cell-free enzyme system such as compartmentalization, metabolic channeling, protein fusion, and co-immobilization strategies. Additionally, we portrayed the novel cell-free enzyme technologies based on encapsulation and immobilization techniques and their development and commercialization. Through this review, we have presented the basics of cell-free enzyme system, the strategies involved in development and operation, and the advantages over conventional processes. Finally, we have addressed some potential directions for the future development and industrialization of cell-free enzyme system.

The structural and functional coordination of glycolytic enzymes in muscle: evidence of a metabolon?

Metabolism sustains life through enzyme-catalyzed chemical reactions within the cells of all organisms. The coupling of catalytic function to the structural organization of enzymes contributes to the kinetic optimization important to tissue-specific and whole-body function. This coupling is of paramount importance in the role that muscle plays in the success of Animalia. The structure and function of glycolytic enzyme complexes in anaerobic metabolism have long been regarded as a major regulatory element necessary for muscle activity and whole-body homeostasis. While the details of this complex remain to be elucidated through in vivo studies, this review will touch on recent studies that suggest the existence of such a complex and its structure. A potential model for glycolytic complexes and related subcomplexes is introduced.

Compartmentalization and metabolic channeling for multienzymatic biosynthesis: practical strategies and modeling approaches

: The construction of efficient enzyme complexes for multienzymatic biosynthesis is of increasing interest in order to achieve maximum yield and to minimize the interference due to shortcomings that are typical for straightforward one-pot multienzyme catalysis. These include product or intermediate feedback inhibition, degeneration, and diffusive losses of reaction intermediates, consumption of co-factors, and others. The main mechanisms in nature to tackle these effects in transient or stable protein associations are the formation of metabolic channeling and microcompartments, processes that are desirable also for multienzymatic biosynthesis in vitro. This chapter provides an overview over two main aspects. First, numerous recent strategies for establishing compartmentalized multienzyme associations and constructed synthetic enzyme complexes are reviewed. Second, the computational methods at hand to investigate and optimize such associations systematically, especially with focus on large multienzyme complexes and metabolic channeling, are discussed. Perspectives on future studies of multienzymatic biosynthesis concerning compartmentalization and metabolic channeling are presented.