scholarly journals LimF is a versatile prenyltransferase catalyzing histidine-C-geranylation on diverse nonnatural substrates

2021 ◽  
Author(s):  
Yuchen Zhang ◽  
Keisuke Hamada ◽  
Dinh Thanh Nguyen ◽  
Sumika Inoue ◽  
Masayuki Satake ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
Structure And Function ◽  
Bioactive Molecules ◽  
Structural Basis ◽  
Peptide Substrate ◽  
Site Specific ◽  
Native Peptide ◽  
Wide Range ◽  
Secondary Function ◽  
And Function

Prenylation plays an important role in diversifying structure and function of secondary metabolites. Although several cyanobactin prenyltransferases have been characterized, their modes of action are mainly limited to the modification of electron-rich hetero atoms. Here we report a unique prenyltransferase originating from Limnothrix sp. CACIAM 69d, referred to as LimF, which catalyzes an unprecedented His-C-geranylation. Interestingly, LimF executes the geranylation on not only its native peptide substrate but also a wide range of exotic peptides, including thioether-closed macrocycles. We have also serendipitously uncovered an ability of Tyr-O-geranylation as the secondary function of LimF, indicating it is an unusual bifunctional prenyltransferase. Crystallographic analysis of LimF complexed with a pentapeptide substrate and a prenyl donor analog provides structural basis for its unique His recognition and its bifunctionality. Lastly, we show the LimF’s prenylation ability on various bioactive molecules containing an imidazole group, highlighting its potential as a versatile biocatalyst for site-specific geranylation.

scholarly journals Synaptic transmission induces site-specific changes in sialylation on N-linked glycoproteins in rat nerve terminals

2020 ◽  
Author(s):  
Inga Boll ◽  
Pia Jensen ◽  
Veit Schwämmle ◽  
Martin R. Larsen
Keyword(s):  
Synaptic Transmission ◽  
Structure And Function ◽  
Synaptic Proteins ◽  
Nerve Terminals ◽  
Membrane Glycoproteins ◽  
Site Specific ◽  
Specific Alteration ◽  
And Function ◽  
Rat Nerve ◽  
Stimulation Of

AbstractSynaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show a novel potential modulator of synaptic transmission, sialylation of N-linked glycosylation. The negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after five seconds depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.

scholarly journals Regulation of OmpA Translation and Shigella dysenteriae Virulence by an RNA Thermometer

2019 ◽  
Vol 88 (3) ◽  
Author(s):  
Erin R. Murphy ◽  
Johanna Roßmanith ◽  
Jacob Sieg ◽  
Megan E. Fris ◽  
Hebaallaha Hussein ◽  
...  
Keyword(s):  
In Silico ◽  
Bacterial Species ◽  
Regulation Of Gene Expression ◽  
Structure And Function ◽  
Shigella Dysenteriae ◽  
Content Type ◽  
Bacterial Physiology ◽  
Wide Range ◽  
Rna Thermometer ◽  
And Function

ABSTRACT RNA thermometers are cis-acting riboregulators that mediate the posttranscriptional regulation of gene expression in response to environmental temperature. Such regulation is conferred by temperature-responsive structural changes within the RNA thermometer that directly result in differential ribosomal binding to the regulated transcript. The significance of RNA thermometers in controlling bacterial physiology and pathogenesis is becoming increasingly clear. This study combines in silico, molecular genetics, and biochemical analyses to characterize both the structure and function of a newly identified RNA thermometer within the ompA transcript of Shigella dysenteriae. First identified by in silico structural predictions, genetic analyses have demonstrated that the ompA RNA thermometer is a functional riboregulator sufficient to confer posttranscriptional temperature-dependent regulation, with optimal expression observed at the host-associated temperature of 37°C. Structural studies and ribosomal binding analyses have revealed both increased exposure of the ribosomal binding site and increased ribosomal binding to the ompA transcript at permissive temperatures. The introduction of site-specific mutations predicted to alter the temperature responsiveness of the ompA RNA thermometer has predictable consequences for both the structure and function of the regulatory element. Finally, in vitro tissue culture-based analyses implicate the ompA RNA thermometer as a bona fide S. dysenteriae virulence factor in this bacterial pathogen. Given that ompA is highly conserved among Gram-negative pathogens, these studies not only provide insight into the significance of riboregulation in controlling Shigella virulence, but they also have the potential to facilitate further understanding of the physiology and/or pathogenesis of a wide range of bacterial species.

scholarly journals Regional, watershed, and site-specific environmental influences on fish assemblage structure and function in western Lake Superior tributaries

2005 ◽  
Vol 62 (6) ◽  
pp. 1254-1270 ◽  
Author(s):  
John C Brazner ◽  
Danny K Tanner ◽  
Naomi E Detenbeck ◽  
Sharon L Batterman ◽  
Stacey L Stark ◽  
...  
Keyword(s):  
Fish Assemblage ◽  
Brook Trout ◽  
Fish Assemblages ◽  
Lake Superior ◽  
Structure And Function ◽  
Assemblage Structure ◽  
Fish Assemblage Structure ◽  
Site Specific ◽  
Western Lake ◽  
And Function

The relative importance of regional, watershed, and in-stream environmental factors on fish assemblage structure and function was investigated in western Lake Superior tributaries. We selected 48 second- and third-order watersheds from two hydrogeomorphic regions to examine fish assemblage response to differences in forest fragmentation, watershed storage, and a number of other watershed, riparian, and in-stream habitat conditions. Although a variety of regional, fragmentation, and storage-related factors had significant influences on the fish assemblages, water temperature appeared to be the single most important environmental factor. We found lower water temperatures and trout–sculpin assemblages at lower fragmentation sites and higher temperatures and minnow–sucker–darter assemblages as storage increased. Factors related to riparian shading and flow separated brook trout streams from brown trout (Salmo trutta) – rainbow trout (Oncorhynchus mykiss) streams. Functionally, fish assemblages at lower fragmentation sites were dominated by cold-water fishes that had low silt tolerance and preferred moderate current speeds, while fishes with higher silt tolerances, warmer temperature preferences, and weaker sustained swimming capabilities were most common at higher storage sites. Our results suggest that site-specific environmental conditions are highly dependent on regional- and watershed-scale characters and that a combination of these factors operates in concert to influence the structure and function of stream fish assemblages.

scholarly journals Design principles of hair-like structures as biological machines

2018 ◽  
Vol 15 (142) ◽  
pp. 20180206 ◽  
Author(s):  
Madeleine Seale ◽  
Cathal Cummins ◽  
Ignazio Maria Viola ◽  
Enrico Mastropaolo ◽  
Naomi Nakayama
Keyword(s):  
Mechanical Properties ◽  
Surface Area ◽  
Large Surface Area ◽  
Structural Basis ◽  
Basic Design ◽  
Form And Function ◽  
Mechanical Unit ◽  
Wide Range ◽  
Range Of Functions ◽  
And Function

Hair-like structures are prevalent throughout biology and frequently act to sense or alter interactions with an organism's environment. The overall shape of a hair is simple: a long, filamentous object that protrudes from the surface of an organism. This basic design, however, can confer a wide range of functions, owing largely to the flexibility and large surface area that it usually possesses. From this simple structural basis, small changes in geometry, such as diameter, curvature and inter-hair spacing, can have considerable effects on mechanical properties, allowing functions such as mechanosensing, attachment, movement and protection. Here, we explore how passive features of hair-like structures, both individually and within arrays, enable diverse functions across biology. Understanding the relationships between form and function can provide biologists with an appreciation for the constraints and possibilities on hair-like structures. Additionally, such structures have already been used in biomimetic engineering with applications in sensing, water capture and adhesion. By examining hairs as a functional mechanical unit, geometry and arrangement can be rationally designed to generate new engineering devices and ideas.

scholarly journals Understanding the impacts of self-shuffling approach on structure and function of shuffled endoglucanase enzyme via MD simulations

2020 ◽  
Vol 45 (2) ◽  
Author(s):  
Aslı Yenenler ◽  
Umut Gerlevik ◽  
Ugur Sezerman
Keyword(s):  
Experimental Studies ◽  
Salt Bridge ◽  
Md Simulations ◽  
Structure And Function ◽  
Computational Approach ◽  
Intramolecular Interactions ◽  
Structural Basis ◽  
Functional Differences ◽  
Structural Differences ◽  
And Function

AbstractObjectiveWe identify the impacts of structural differences on functionality of EG3_S2 endoglucanase enzyme with MD studies. The results of previous experimental studies have been explained in details with computational approach. The objective of this study is to explain the functional differences between shuffled enzyme (EG3_S2) and its native counterpart (EG3_nat) from Trichoderma reseei, via Molecular Dynamics approach.Materials and methodsFor this purpose, we performed MD simulations along 30 ns at three different reaction temperatures collected as NpT ensemble, and then monitored the backbone motion, flexibilities of residues, and intramolecular interactions of EG3_S2 and EG3_nat enzymes.ResultsAccording to MD results, we conclude that EG3_S2 and EG3_nat enzymes have unique RMSD patterns, e.g. RMSD pattern of EG3_S2 is more dynamic than that of EG3_nat at all temperatures. In addition to this dynamicity, EG3_S2 establishes more salt bridge interactions than EG3_nat.ConclusionBy taking these results into an account with the preservation of catalytic Glu residues in a proper manner, we explain the structural basis of differences between shuffled and native enzyme via molecular dynamic studies.

scholarly journals Structural Basis of Redox Signaling in Photosynthesis: Structure and Function of Ferredoxin:thioredoxin Reductase and Target Enzymes

2004 ◽  
Vol 79 (3) ◽  
pp. 233-248 ◽  
Author(s):  
Shaodong Dai ◽  
Kenth Johansson ◽  
Myroslawa Miginiac-Maslow ◽  
Peter Schürmann ◽  
Hans Eklund
Keyword(s):  
Redox Signaling ◽  
Structure And Function ◽  
Structural Basis ◽  
And Function ◽  
Ferredoxin:Thioredoxin Reductase

Commentary on “Reflections on culture, structure and function of an intensive support service centred on positive behavioural support”

2016 ◽  
Vol 21 (4) ◽  
pp. 212-219 ◽  
Author(s):  
Sandy Toogood
Keyword(s):  
Support Service ◽  
Structure And Function ◽  
Content Type ◽  
Behavioural Support ◽  
Wide Range ◽  
Service Models ◽  
History Of ◽  
Positive Behaviour Support ◽  
The Uk ◽  
And Function

Purpose The purpose of this paper is to provide a commentary on Patterson and Berry’s paper “Reflections on culture, structure and function of an intensive support service centred on positive behavioural support”. Design/methodology/approach This paper reviews key ideas presented in Patterson and Berry’s article relative to the recent history of service delivery in the UK and the growing interest being shown in positive behaviour support. Findings Patterson and Berry’s article adds to a modest literature on specialist support services and should stimulate further descriptions of service models and the concepts underpinning them. Originality/value The literature on specialist support service models is limited and this addition should be relevant to a wide range of clinicians, consumers and commissioners.

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