scholarly journals Plant asparaginyl endopeptidases and their structural determinants of function

2021 ◽  
Author(s):  
Samuel G. Nonis ◽  
Joel Haywood ◽  
Joshua S. Mylne
Keyword(s):  
Protein Sequence ◽  
Biological Systems ◽  
Catalytic Efficiency ◽  
Circular Permutation ◽  
Structural Determinants ◽  
Pharmaceutical Applications

Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i) routine cleavage by bond hydrolysis, (ii) peptide maturation, including macrocyclisation by a cleavage-coupled intramolecular transpeptidation and (iii) circular permutation involving separate cleavage and transpeptidation reactions resulting in a major reshuffling of protein sequence. AEPs differ in their preference for cleavage or transpeptidation reactions, catalytic efficiency, and preference for asparagine or aspartate target residues. We look at structural analyses of various AEPs that have laid the groundwork for identifying important determinants of AEP function in recent years, with much of the research impetus arising from the potential biotechnological and pharmaceutical applications.

scholarly journals Small-angle neutron scattering reveals the assembly mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase

2014 ◽  
Vol 70 (11) ◽  
pp. 2983-2993 ◽  
Author(s):  
Alexandre Appolaire ◽  
Eric Girard ◽  
Matteo Colombo ◽  
M. Asunción Durá ◽  
Martine Moulin ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Quaternary Structure ◽  
De Novo ◽  
Biological Systems ◽  
Catalytic Efficiency ◽  
Building Blocks ◽  
Assembly Pathways

The specific self-association of proteins into oligomeric complexes is a common phenomenon in biological systems to optimize and regulate their function. However,de novostructure determination of these important complexes is often very challenging for atomic-resolution techniques. Furthermore, in the case of homo-oligomeric complexes, or complexes with very similar building blocks, the respective positions of subunits and their assembly pathways are difficult to determine using many structural biology techniques. Here, an elegant and powerful approach based on small-angle neutron scattering is applied, in combination with deuterium labelling and contrast variation, to elucidate the oligomeric organization of the quaternary structure and the assembly pathways of 468 kDa, hetero-oligomeric and symmetricPyrococcus horikoshiiTET2–TET3 aminopeptidase complexes. The results reveal that the topology of thePhTET2 andPhTET3 dimeric building blocks within the complexes is not casual but rather suggests that their quaternary arrangement optimizes the catalytic efficiency towards peptide substrates. This approach bears important potential for the determination of quaternary structures and assembly pathways of large oligomeric and symmetric complexes in biological systems.

scholarly journals Discovery of an ultra-specific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway

2020 ◽  
pp. jbc.RA120.015631
Author(s):  
Lambros J. Tassoulas ◽  
Mikael H. Elias ◽  
Lawrence P. Wackett
Keyword(s):  
Human Urine ◽  
Active Site ◽  
Protein Sequence ◽  
Endophytic Bacteria ◽  
Catalytic Efficiency ◽  
Anthropogenic Sources ◽  
Substrate Selectivity ◽  
Bacterial Genomes ◽  
Protein Sequence Homology ◽  
Site Mutagenesis

Triuret (carbonyldiurea) is an impurity found in industrial urea fertilizer (<0.1% w/w) that is applied, worldwide, around 300 million pounds each year on agricultural lands. In addition to anthropogenic sources, endogenous triuret has been identified in amoeba and human urine, the latter being diagnostic for hypokalemia. The present study is the first to describe the metabolic breakdown of triuret, which funnels into biuret metabolism. We identified the gene responsible for triuret decomposition (trtA) in bacterial genomes, clustered with biuH, that encodes biuret hydrolase and has close protein sequence homology. TrtA is a member of the isochorismatase-like hydrolase protein family (IHL), similarly to BiuH, and has a catalytic efficiency (kcat/KM) of 6 x 105 (M-1s-1), a KM for triuret of 20 μM, and exquisite substrate specificity. Indeed, TrtA has four orders of magnitude less activity with biuret. Crystal structures of TrtA in apo and holo form were solved and compared to the BiuH structure. The high substrate selectivity was found to be conveyed by second shell residues around each active site. Mutagenesis of residues conserved in TrtA to the alternate consensus found in BiuHs revealed residues critical to triuret hydrolase activity but no single mutant evolved more biuret activity and likely a combination of mutations is required to interconvert between TrtA, BiuH functions. TrtA-mediated triuret metabolism is relatively rare in recorded genomes (1-2%), but is largely found in plant-associated, nodulating and endophytic bacteria. This study suggests functions for triuret hydrolase in certain eukaryotic intermediary processes and prokaryotic intermediary or biodegradative metabolism

Learning From Biological Systems: Novel Routes to Biomimetic Synthesis of Ordered Silica Structures

1999 ◽  
Vol 599 ◽  
Author(s):  
Jennifer N. Chal ◽  
Katsuhiko Shimizu ◽  
Yan Zhou ◽  
Sean C. Christiansen ◽  
Bradley F. Chmelka ◽  
...  
Keyword(s):  
Structural Control ◽  
Catalytic Mechanism ◽  
Ambient Pressure ◽  
Biological Systems ◽  
Dry Weight ◽  
Biomimetic Synthesis ◽  
Skeletal System ◽  
Structural Determinants ◽  
Axial Filament ◽  
Block Copolypeptides

AbstractBiological systems have evolved mechanisms that precisely control inorganic structures on both the micro- and nanoscale, operating at ambient pressures and temperatures. In both the calcium carbonate, calcium phosphate and silicon dioxide utilizing organisms, proteins and polysaccharides have been found to play integral roles in the organization of these biominerals[1–3]. The organic constituents generally have been thought to act as direct templates or modulators for the deposition of the particular mineral. We have explored the synthesis and structural control of silica by the marine sponge, Tethya aurantia. Needles of amorphous silica comprise the skeletal system of this organism, representing 75% of the dry weight of the organism. These glassy needles, called spicules, are 2 mm in length and 30 μn in width[4,5]. We have characterized the structure, genetics and functions of the proteins that form an occluded axial filament within each silica spicule. Based on our discovery, a unique structure-directing catalytic mechanism exhibited by these protein filaments, and the structural determinants responsible for the catalytic activity, we have designed novel block copolypeptides that catalyze and spatially direct he condensation of silicon alkoxides to form organized silica structures ranging from transparent spheres to lath-like structures at ambient pressure, low temperature and neutral pH.

Transmission Electron Microscopy of Protein Macromolecules

1971 ◽  
Vol 29 ◽  
pp. 424-425
Author(s):  
Henry S. Slayter
Keyword(s):  
Biological Systems ◽  
Metal Vapor ◽  
Resolving Power ◽  
Electron Microscopic ◽  
Chemical Methods ◽  
Molecular Weights ◽  
The Past ◽  
Physical Chemical ◽  
Transmission Electron

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.

Freeze-fracture cytochemistry: A goal set by Russell Steere in 1957

1993 ◽  
Vol 51 ◽  
pp. 60-61
Author(s):  
Nicholas J Severs
Keyword(s):  
Chemical Nature ◽  
Biological Systems ◽  
Freeze Fracture ◽  
Structural Components ◽  
Major Goal ◽  
Membrane Biology ◽  
Routine Application ◽  
The Future ◽  
Freeze Etching

In his pioneering demonstration of the potential of freeze-etching in biological systems, Russell Steere assessed the future promise and limitations of the technique with remarkable foresight. Item 2 in his list of inherent difficulties as they then stood stated “The chemical nature of the objects seen in the replica cannot be determined”. This defined a major goal for practitioners of freeze-fracture which, for more than a decade, seemed unattainable. It was not until the introduction of the label-fracture-etch technique in the early 1970s that the mould was broken, and not until the following decade that the full scope of modern freeze-fracture cytochemistry took shape. The culmination of these developments in the 1990s now equips the researcher with a set of effective techniques for routine application in cell and membrane biology.Freeze-fracture cytochemical techniques are all designed to provide information on the chemical nature of structural components revealed by freeze-fracture, but differ in how this is achieved, in precisely what type of information is obtained, and in which types of specimen can be studied.

Seeking to uncover biology's chemical roots

2019 ◽  
Vol 3 (5) ◽  
pp. 435-443 ◽  
Author(s):  
Addy Pross
Keyword(s):  
Environmental Changes ◽  
Biological Systems ◽  
Significant Development ◽  
The Road ◽  
Physical Chemical ◽  
Systems Chemistry ◽  
Biological World ◽  
Inanimate Matter ◽  
The Origin Of Life ◽  
Opening Up

Despite the considerable advances in molecular biology over the past several decades, the nature of the physical–chemical process by which inanimate matter become transformed into simplest life remains elusive. In this review, we describe recent advances in a relatively new area of chemistry, systems chemistry, which attempts to uncover the physical–chemical principles underlying that remarkable transformation. A significant development has been the discovery that within the space of chemical potentiality there exists a largely unexplored kinetic domain which could be termed dynamic kinetic chemistry. Our analysis suggests that all biological systems and associated sub-systems belong to this distinct domain, thereby facilitating the placement of biological systems within a coherent physical/chemical framework. That discovery offers new insights into the origin of life process, as well as opening the door toward the preparation of active materials able to self-heal, adapt to environmental changes, even communicate, mimicking what transpires routinely in the biological world. The road to simplest proto-life appears to be opening up.

Sign in / Sign up

Export Citation Format

Share Document