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PubMed Journal Database | Protein science : a publication of the Protein Society RSS

09:17 EDT 20th June 2019 | BioPortfolio

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Showing PubMed Articles 1–25 of 216 from Protein science : a publication of the Protein Society

A Cryptic Activity in the Nudix Hydrolase Superfamily.

The Nudix hydrolase superfamily is identified by a conserved cassette of 23 amino acids, and it is characterized by its pyrophosphorylytic activity on a wide variety of nucleoside diphosphate derivatives. Of the 13 members of the family in E.coli, only 1, Orf180, has not been identified with a substrate, although a host of nucleoside diphosphate compounds have been tested. Several reports have noted a strong similarity in the three dimensional structure of the unrelated enzyme, isopentenyl diphosphate isome...

Inaccurate secondary structure predictions often indicate protein fold switching.

Although most proteins conform to the classical one-structure/one-function paradigm, an increasing number of proteins with dual structures and functions have been discovered. In response to cellular stimuli, such proteins undergo structural changes sufficiently dramatic to remodel even their secondary structures and domain organization. This "fold-switching" capability fosters protein multi-functionality, enabling cells to establish tight control over various biochemical processes. Accurate predictions of f...

Structural insight into the high reduction potentials observed for Fusobacterium nucleatum flavodoxin.

Flavodoxins are small FMN-containing proteins that mediate a variety of electron transfer processes. The primary sequence of flavodoxin from Fusobacterium nucleatum, a pathogenic oral bacterium, is marked with a number of distinct features including a glycine to lysine (K13) substitution in the highly conserved phosphate binding loop (T/S-X-T-G-X-T), variation in the aromatic residues that sandwich the FMN cofactor, and a more even distribution of acidic and basic residues. The E (oxidized/semiquinone; -43 ...

Sequence Composition versus Sequence Order in the Cryoprotective Function of an Intrinsically Disordered Stress-Response Protein.

Intrinsically disordered stress proteins have been shown to act as chaperones, protecting proteins from damage caused by stresses such as freezing and thawing. Dehydration proteins (dehydrins) are intrinsically disordered stress proteins that are found in almost all land plants. They consist of a variable number of the short, semi-conserved, Y-, S- and K-segments, with longer stretches of poorly conserved sequences in between. Previous studies have provided conflicting views on the details of the dehydrin c...

Polycomb Repressive 2 Complex-Molecular Mechanisms of Function.

Numerous molecular processes conduct epigenetic regulation of protein transcription to maintain cell specification. In this review, we discuss molecular mechanisms of the Polycomb group (PcG) of proteins and its enzymatic role in epigenetics. More specifically, we focus on the Polycomb repressive complex 2 (PRC2) and the effects of its repressive marker. We have compiled information regarding the biological structure and how that impacts the stability of the complex. In addition, we examined functions of th...

Chimeric dihydrofolate reductases (DHFR) display properties of modularity and biophysical diversity.

While reverse genetics and functional genomics have long affirmed the role of individual mutations in determining protein function, there have been fewer studies addressing how larger-scaled changes in protein sequences, such as in entire modular segments, influence protein function and evolution. Given how recombination can reassort protein sequences, these types of changes may play an underappreciated role in how novel protein functions evolve in nature. Such studies could aid our understanding of whether...

Predicting and validating a model of Suppressor of IKKepsilon through biophysical characterization.

Suppressor of IKKepsilon (SIKE) is a 207 residue protein that is implicated in the TLR3-TANK binding kinase 1-mediated response to viral infection. SIKE's function in this pathway is unknown, but SIKE forms interactions with two distinct cytoskeletal proteins, α-actinin and tubulin, and SIKE knockout reduces cell migration. As structure informs function and in the absence of solved structural homologs, our studies were directed toward creating a structural model of SIKE through biochemical and biophysical ...

Kinetic vs. Thermodynamic Control of Mutational Effects on Protein Homeostasis: A Perspective from Computational Modeling and Experiment.

The effect of mutations in individual proteins on protein homeostasis, or "proteostasis", can in principle depend on the mutations' effects on the thermodynamics or kinetics of folding, or both. Here, we explore this issue using a computational model of in vivo protein folding that we call FoldEcoSlim. Our model predicts that kinetic vs. thermodynamic control of mutational effects on proteostasis hinges on the relationship between how fast a protein's folding reaction reaches equilibrium and a critical time...

Selection and Analyses of Variants of A Designed Protein Suggest Importance of Hydrophobicity of Partially Buried Sidechains for Protein Stability at High Temperatures.

Computationally designed proteins of high stability provide specimen in addition to natural proteins for the study of sequence-structure stability relationships at the very high end of protein stability spectrum. The melting temperature of E_1r26, a protein we previously designed using the ABACUS (A Backbone-based Amino aCid Usage Survey) sequence design program, is above 110 °C, more than 50 °C higher than that of the natural thioredoxin protein whose backbone (PDB ID 1r26) has been used as the design ta...

Plasticity and transient binding are key ingredients of the periplasmic chaperone network.

SurA, Skp, FkpA and DegP constitute a chaperone network that ensures biogenesis of outer membrane proteins (OMP)s in Gram-negative bacteria. Both Skp and FkpA are holdases that prevent the self-aggregation of unfolded OMPs, whereas SurA accelerates folding and DegP is a protease. None of these chaperones is essential, and we address here how functional plasticity is manifested in nine known null strains. Using a comprehensive computational model of this network termed OMPBioM, our results suggest that a thr...

Substrate selection by the proteasome through initiation regions.

Proteins in the cell have to be eliminated once their function is no longer desired or they become damaged. Most regulated protein degradation is achieved by a large enzymatic complex called the proteasome. Many proteasome substrates are targeted for degradation by the covalent attachment of ubiquitin molecules. Ubiquitinated proteins can be bound by the proteasome, but for proteolysis to occur the proteasome needs to find a disordered tail somewhere in the target at which it initiates degradation. The init...

Tracing the evolution of novel features of human Toll-like receptor 4.

Toll-like receptor 4 (TLR4) is a critical innate immune protein that activates inflammation in response to extracellular cues. Much of the work to understand how the protein works in humans has been done using mouse models. Although human and mouse TLR4 have many shared features, they have also diverged significantly since their last common ancestor, acquiring 277 sequence differences. Functional differences include the extent of ligand-independent activation, whether lipid IVa acts as an antagonist or agon...

Protein Science Best Paper Awards to Yu-ming Huang and Abhay Thakur.

From fluorescent proteins to fluorogenic RNAs: tools for imaging cellular macromolecules.

The explosion in genome-wide sequencing has revealed that non-coding RNAs are ubiquitous and highly conserved in biology. New molecular tools are needed for their study in live cells. Fluorescent RNA-small molecule complexes have emerged as powerful counterparts to fluorescent proteins, which are well established, universal tools in the study of proteins in cell biology. No naturally fluorescent RNAs are known; all current fluorescent RNA tags are in vitro evolved or engineered molecules that bind a conditi...

Function and solution structure of the Arabidopsis thaliana RALF8 peptide.

We report the recombinant preparation from Escherichia coli cells of samples of two closely related, small, secreted cysteine-rich plant peptides: Rapid ALkalinization Factor-1 (RALF1) and Rapid ALkalinization Factor-8 (RALF8). Purified samples of the native sequence of RALF8 exhibited well-resolved NMR spectra and also biological activity through interaction with a plant receptor kinase, cytoplasmic calcium mobilization, and in vivo root growth suppression. By contrast, RALF1 could only be isolated from in...

Biogenesis, quality control and structural dynamics of proteins as explored in living cells via site-directed photo-crosslinking.

Protein biogenesis and quality control are essential for maintaining a functional pool of proteins and involve numerous protein factors that dynamically and transiently interact with each other and with the substrate proteins in living cells. Conventional methods are hardly effective for studying such dynamic, transient, and weak protein-protein interactions as occur in cells. Herein we review how the site-directed photo-crosslinking approach, which relies on the genetic incorporation of a photo-reactive un...

Bismaleimide cross-linked anthrax toxin forms functional octamers with high-specificity in tumor targeting.

In recent years anthrax toxin has been re-engineered to act as a highly-specific anti-angiogenic cancer therapeutic, shown to kill tumors in animal models. This has been achieved by modifying protective antigen (PA) so that its activation and toxicity require the presence of two proteases, matrix metalloproteinase (MMP) and urokinase plasminogen activator (uPA), which are upregulated in tumor microenvironments. These therapeutics consist of intercomplementing PA variants, which are individually nontoxic, bu...

Variation in assembly stoichiometry in non-metazoan homologs of the hub domain of Ca2+/Calmodulin-dependent protein kinase II.

The multi-subunit Ca /calmodulin-dependent protein kinase II (CaMKII) holoenzyme plays a critical role in animal learning and memory. The kinase domain of CaMKII is connected by a flexible linker to a C-terminal hub domain that assembles into a 12- or 14-subunit scaffold that displays the kinase domains around it. Studies on CaMKII suggest that the stoichiometry and dynamic assembly/disassembly of hub oligomers may be important for CaMKII regulation. Although CaMKII is a metazoan protein, genes encoding pre...

A strategy for the identification of protein architectures directly from ion mobility mass spectrometry data reveals stabilizing subunit interactions in light harvesting complexes.

Biotechnological applications of protein complexes require detailed information about their structure and composition, which can be challenging to obtain for proteins from natural sources. Prominent examples are the ring-shaped phycoerythrin (PE) and phycocyanin (PC) complexes isolated from the light-harvesting antennae of red algae and cyanobacteria. Despite their wide-spread use as fluorescent probes in biotechnology and medicine, the structures and interactions of their non-crystallizable central subunit...

Human Pantothenate Kinase 4 (PANK4) is a Pseudo-Pantothenate Kinase.

Pantothenate kinase generates 4'-phosphopantothenate in the first and rate-determining step of coenzyme A (CoA) biosynthesis. The human genome encodes three well-characterized and nearly identical pantothenate kinases (PANK1-3) plus a putative bifunctional protein (PANK4) with a predicted amino-terminal pantothenate kinase domain fused to a carboxy-terminal phosphatase domain. Structural and phylogenetic analyses show that all active, characterized PANKs contain the key catalytic residues Glu138 and Arg207 ...

Zinc finger domain of the human DTX protein adopts a unique RING fold.

The Deltex (DTX) family is involved in ubiquitination and acts as Notch signaling modifiers for controlling cell fate determination. DTX promotes the development of the ubiquitin chain via its RING finger (DTX_RING). In this study, the solution structure of DTX_RING was determined using nuclear magnetic resonance (NMR). Moreover, by experiments with a metallochromic indicator, we spectrophotometrically estimated the stoichiometry of zinc ions and found that DTX_RING possesses zinc-binding capabilities. The ...

The T99K variant of glycosylasparaginase shows a new structural mechanism of the genetic disease aspartylglucosaminuria.

Aspartylglucosaminuria (AGU) is an inherited disease caused by mutations in a lysosomal amidase called aspartylglucosaminidase (AGA) or glycosylasparaginase (GA). This disorder results in an accumulation of glycoasparagines in the lysosomes of virtually all cell types; with severe clinical symptoms affecting the central nervous system, skeletal abnormalities, and connective tissue lesions. GA is synthesized as a single-chain precursor that requires an intramolecular autoprocessing to form a mature amidase. ...

The Vexing Complexity of the Amyloidogenic Pathway.

The role of the amyloidogenic pathway in the etiology of Alzheimer's disease (AD), particularly the common sporadic late onset forms of the disease, is controversial. To some degree, this is a consequence of the failure of drug and therapeutic antibody trials based either on targeting the proteases in this pathway or its amyloid end products. Here, we explore the formidable complexity of the biochemistry and cell biology associated with this pathway. For example, we review evidence that the immediate precur...

An ensemble of lipoxygenase structures reveals novel conformations of the Fe coordination sphere.

The regio- and stereo- specific oxygenation of polyunsaturated fatty acids (PUFA) is catalyzed by lipoxygenases (LOX); both Fe and Mn forms of the enzyme have been described. Structural elements of the Fe and Mn coordination spheres and the helical catalytic domain in which the metal center resides are highly conserved. However, animal, plant and microbial LOX each have distinct features. We report five crystal structures of a LOX from the fungal plant pathogen Fusarium graminearum. This LOX displays a nove...

Lipid Composition and Macromolecular Crowding Effects on CYP2J2-Mediated Drug Metabolism in Nanodiscs.

Lipid composition and macromolecular crowding are key external effectors of protein activity and stability whose role varies between different proteins. Therefore, it is imperative to study their effects on individual protein function. CYP2J2 is a membrane-bound cytochrome P450 in the heart involved in the metabolism of fatty acids and xenobiotics. In order to facilitate this metabolism, cytochrome P450 reductase (CPR), transfers electrons to CYP2J2 from NADPH. Herein, we use nanodiscs to show that lipid co...


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