scholarly journals Metzincin's canonical methionine is responsible for the structural integrity of the zinc-binding site

2009 ◽  
Vol 390 (9) ◽  
Author(s):  
Anselm E. Oberholzer ◽  
Mario Bumann ◽  
Thomas Hege ◽  
Santina Russo ◽  
Ulrich Baumann
Keyword(s):  
Structural Integrity ◽  
Polypeptide Chain ◽  
Consensus Sequence ◽  
Large Body ◽  
Zinc Binding ◽  
Side Chain ◽  
Type I ◽  
Gram Negative Bacteria ◽  
Zinc Binding Site ◽  
Binding Consensus Sequence

Abstract The metzincins constitute a subclan of metalloproteases possessing a HEXXHXXGXXH/D zinc-binding consensus sequence where the three histidines are zinc ligands and the glutamic acid is the catalytic base. A completely conserved methionine is located downstream of this motif. Families of the metzincin clan comprise, besides others, astacins, adamalysins proteases, matrix metallo-proteases, and serralysins. The latter are extracellular 50 kDa proteases secreted by Gram-negative bacteria via a type I secretion system. While there is a large body of structural and biochemical information available, the function of the conserved methionine has not been convincingly clarified yet. Here, we present the crystal structures of a number of mutants of the serralysin member protease C with the conserved methionine being replaced by Ile, Ala, and His. Together with our former report on the leucine and cysteine mutants, we demonstrate here that replacement of the methionine side chain results in an increasing distortion of the zinc-binding geometry, especially pronounced in the χ2 angles of the first and third histidine of the consensus sequence. This is correlated with an increasing loss of proteolytic activity and a sharp increase of flexibility of large segments of the polypeptide chain.

Polypeptides Folding: Rules for the Calculation of the Backbone Dihedral Angles φ starting from the Amino Acid Sequence

2020 ◽  
Author(s):  
Michele Larocca
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Theoretical Approach ◽  
Polypeptide Chain ◽  
Hydrophobic Effect ◽  
Side Chain ◽  
Dihedral Angles ◽  
Mechanical Forces ◽  
Specific Chemical

<p>Protein folding is strictly related to the determination of the backbone dihedral angles and depends on the information contained in the amino acid sequence as well as on the hydrophobic effect. To date, the type of information embedded in the amino acid sequence has not yet been revealed. The present study deals with these problematics and aims to furnish a possible explanation of the information contained in the amino acid sequence, showing and reporting rules to calculate the backbone dihedral angles φ. The study is based on the development of mechanical forces once specific chemical interactions are established among the side chain of the residues in a polypeptide chain. It aims to furnish a theoretical approach to predict backbone dihedral angles which, in the future, may be applied to computational developments focused on the prediction of polypeptide structures.</p>

scholarly journals Current Understanding of the Structure, Stability and Dynamic Properties of Amyloid Fibrils

2021 ◽  
Vol 22 (9) ◽  
pp. 4349
Author(s):  
Eri Chatani ◽  
Keisuke Yuzu ◽  
Yumiko Ohhashi ◽  
Yuji Goto
Keyword(s):  
Amyloid Fibrils ◽  
Polypeptide Chain ◽  
Dynamic Properties ◽  
Protein Molecule ◽  
Side Chain ◽  
Structure Stability ◽  
Side Chains ◽  
Precise Control ◽  
Functional Amyloids ◽  
Structural Architecture

Amyloid fibrils are supramolecular protein assemblies represented by a cross-β structure and fibrous morphology, whose structural architecture has been previously investigated. While amyloid fibrils are basically a main-chain-dominated structure consisting of a backbone of hydrogen bonds, side-chain interactions also play an important role in determining their detailed structures and physicochemical properties. In amyloid fibrils comprising short peptide segments, a steric zipper where a pair of β-sheets with side chains interdigitate tightly is found as a fundamental motif. In amyloid fibrils comprising longer polypeptides, each polypeptide chain folds into a planar structure composed of several β-strands linked by turns or loops, and the steric zippers are formed locally to stabilize the structure. Multiple segments capable of forming steric zippers are contained within a single protein molecule in many cases, and polymorphism appears as a result of the diverse regions and counterparts of the steric zippers. Furthermore, the β-solenoid structure, where the polypeptide chain folds in a solenoid shape with side chains packed inside, is recognized as another important amyloid motif. While side-chain interactions are primarily achieved by non-polar residues in disease-related amyloid fibrils, the participation of hydrophilic and charged residues is prominent in functional amyloids, which often leads to spatiotemporally controlled fibrillation, high reversibility, and the formation of labile amyloids with kinked backbone topology. Achieving precise control of the side-chain interactions within amyloid structures will open up a new horizon for designing useful amyloid-based nanomaterials.

Protein kinase CK2: a newcomer in the ‘druggable kinome’

2006 ◽  
Vol 34 (6) ◽  
pp. 1303-1306 ◽  
Author(s):  
M.A. Pagano ◽  
L. Cesaro ◽  
F. Meggio ◽  
L.A. Pinna
Keyword(s):  
Protein Kinase ◽  
Consensus Sequence ◽  
Side Chain ◽  
Constitutive Activity ◽  
Eukaryotic Protein Kinase ◽  
Pathological Conditions ◽  
Cardiovascular Pathologies ◽  
Special Circumstances ◽  
Kinase Ck2 ◽  
Different Sources

The acronym CK2 (derived from the misnomer ‘casein kinase’ 2) denotes one of the most pleiotropic members of the eukaryotic protein kinase superfamily, characterized by an acidic consensus sequence in which a carboxylic acid (or pre-phosphorylated) side chain at position n+3 relative to the target serine/threonine residue plays a crucial role. The latest repertoire of CK2 substrates includes approx. 300 proteins, but the analysis of available phosphopeptide databases from different sources suggests that CK2 alone may be responsible for the generation of a much larger proportion (10–20%) of the eukaryotic phosphoproteome. Although for the time being CK2 is not included among protein kinases whose inhibitors are in clinical practice or in advanced clinical trials, evidence is accumulating that elevated CK2 constitutive activity co-operates to induce a number of pathological conditions, including cancer, infectious diseases, neurodegeneration and cardiovascular pathologies. The development and usage of cell-permeant, selective inhibitors discloses a scenario whereby CK2 plays a global anti-apoptotic role, which under special circumstances may lead to untimely and pathogenic cell survival.

scholarly journals ICSBP-mediated immune protection against BCR-ABL–induced leukemia requires the CCL6 and CCL9 chemokines

Blood ◽  
2009 ◽  
Vol 113 (16) ◽  
pp. 3813-3820 ◽  
Author(s):  
Valentina Nardi ◽  
Olaia Naveiras ◽  
Mohammad Azam ◽  
George Q. Daley
Keyword(s):  
Murine Model ◽  
Consensus Sequence ◽  
Myelogenous Leukemia ◽  
Transformed Cells ◽  
Type I ◽  
Immune Protection ◽  
Immune Mechanism ◽  
Type I Ifns ◽  
New Strategies

Abstract Interferon (IFN) is effective at inducing complete remissions in patients with chronic myelogenous leukemia (CML), and evidence supports an immune mechanism. Here we show that the type I IFNs (alpha and beta) regulate expression of the IFN consensus sequence-binding protein (ICSBP) in BCR-ABL–transformed cells and as shown previously for ICSBP, induce a vaccine-like immunoprotective effect in a murine model of BCR-ABL–induced leukemia. We identify the chemokines CCL6 and CCL9 as genes prominently induced by the type I IFNs and ICSBP, and demonstrate that these immunomodulators are required for the immunoprotective effect of ICSBP expression. Insights into the role of these chemokines in the antileukemic response of IFNs suggest new strategies for immunotherapy of CML.

scholarly journals MisR/MisS Two-Component Regulon in Neisseria meningitidis

2007 ◽  
Vol 76 (2) ◽  
pp. 704-716 ◽  
Author(s):  
Yih-Ling Tzeng ◽  
Charlene M. Kahler ◽  
Xinjian Zhang ◽  
David S. Stephens
Keyword(s):  
Neisseria Meningitidis ◽  
Target Genes ◽  
Inner Core ◽  
Consensus Sequence ◽  
Meningococcal Infection ◽  
Type I ◽  
Mobility Shift ◽  
Iron Assimilation ◽  
Wide Range ◽  
Two Component

ABSTRACT Two-component regulatory systems are involved in processes important for bacterial pathogenesis. Inactivation of the misR/misS system in Neisseria meningitidis results in the loss of phosphorylation of the lipooligosaccharide inner core and causes attenuation in a mouse model of meningococcal infection. One hundred seventeen (78 up-regulated and 39 down-regulated) potential regulatory targets of the MisR/MisS (MisR/S) system were identified by transcriptional profiling of the NMBmisR mutant and the parental wild-type meningococcal strain NMB. The regulatory effect was further confirmed in a subset of target genes by quantitative real-time PCR and β-galactosidase transcriptional fusion reporter assays. The MisR regulon includes genes encoding proteins necessary for protein folding in the bacterial cytoplasm and periplasm, transcriptional regulation, metabolism, iron assimilation, and type I protein transport. Mutation in the MisR/S system caused increased sensitivity to oxidative stress and also resulted in decreased susceptibility to complement-mediated killing by normal human serum. To identify the direct targets of MisR regulation, electrophoretic mobility shift assays were carried out using purified MisR-His6 protein. Among 22 genes examined, misR directly interacted with 14 promoter regions. Six promoters were further investigated by DNase I protection assays, and a MisR-binding consensus sequence was proposed. Thus, the direct regulatory targets of MisR and the minimal regulon of the meningococcal MisR/S two-component signal transduction system were characterized. These data indicate that the MisR/S system influences a wide range of biological functions in N. meningitidis either directly or via intermediate regulators.

Rashes with Ampicillin

1980 ◽  
Vol 1 (7) ◽  
pp. 197-201
Author(s):  
Michael J. Kraemer ◽  
Arnold L. Smith
Keyword(s):  
Penicillin G ◽  
Side Chain ◽  
Gram Negative Bacteria ◽  
Acid Moiety ◽  
Structure Activity ◽  
Body Tissues ◽  
The Family ◽  
Acyl Side Chain ◽  
Penicillanic Acid ◽  
Lactam Ring

Ampicillin, first introduced in 1961, has probably become the most widely used penicillin in clinical pediatrics. STRUCTURE ACTIVITY RELATIONSHIPS All penicillins contain the 6-amino penicillanic acid moiety (Fig 1). Its structure includes a thiazolidine ring (A), a β-lactam ring (B), the source of antibacterial activity, and an acyl side chain (R), containing a variety of substitutions creating the family of semisynthetic penicillins. The only difference between ampicillin and penicillin G is the presence of an amino group in the acyl side chain (Fig 1). PHARMACOLOGY AND BACTERIOLOGY Ampicillin is a semisynthetic penicillin, active against Streptococus pneumoniae and certain Gram-negative bacteria, including most Haemophilus influenzae, Escherichia coli, and certain Proteus species. Compared to penicillin G, it has increased stability in acid solutions: a property facilitating oral administration and absorption. It penetrates into most body tissues; effective entry into CSF, however, occurs only with inflamed meninges. The serum half-life with normal renal function varies from four hours in newborns1 to 1.3 hours in adults.2 Ampicillin can cause an allergic, or nonallergic skin rash (Fig 2). ALLERGY Allergy (for the purposes of this discussion) is defined as a specific immunologic interaction, between either antigen and antibody, or antigen with a sensitized lymphocyte, resulting in a clinically deleterious effect. Implicit is a prior contact with the antigen.

scholarly journals Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation

2018 ◽  
Vol 116 (2) ◽  
pp. 528-533 ◽  
Author(s):  
Ivan B. Lomakin ◽  
Sergey E. Dmitriev ◽  
Thomas A. Steitz
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Translation Initiation ◽  
Zinc Ion ◽  
Zinc Binding ◽  
Ion Binding ◽  
Binding Interface ◽  
Zinc Binding Site ◽  
Reading Frames ◽  
Zinc Ion Binding

The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR’s MCT-1–binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.

scholarly journals Vibrio cholerae VibF Is Required for Vibriobactin Synthesis and Is a Member of the Family of Nonribosomal Peptide Synthetases

2000 ◽  
Vol 182 (6) ◽  
pp. 1731-1738 ◽  
Author(s):  
Joan R. Butterton ◽  
Michael H. Choi ◽  
Paula I. Watnick ◽  
Patricia A. Carroll ◽  
Stephen B. Calderwood
Keyword(s):  
Outer Membrane ◽  
Vibrio Cholerae ◽  
Consensus Sequence ◽  
Membrane Receptor ◽  
Transcriptional Level ◽  
Outer Membrane Receptor ◽  
Chromosomal Dna ◽  
E Coli ◽  
Binding Consensus Sequence

ABSTRACT A 7.5-kbp fragment of chromosomal DNA downstream of theVibrio cholerae vibriobactin outer membrane receptor,viuA, and the vibriobactin utilization gene,viuB, was recovered from a Sau3A lambda library of O395 chromosomal DNA. By analogy with the genetic organization of the Escherichia coli enterobactin gene cluster, in which the enterobactin biosynthetic and transport genes lie adjacent to the enterobactin outer membrane receptor, fepA, and the utilization gene, fes, the cloned DNA was examined for the ability to restore siderophore synthesis to E. coli entmutants. Cross-feeding studies demonstrated that an E. coli entF mutant complemented with the cloned DNA regained the ability to synthesize enterobactin and to grow in low-iron medium. Sequence analysis of the cloned chromosomal DNA revealed an open reading frame downstream of viuB which encoded a deduced protein of greater than 2,158 amino acids, homologous to Yersinia sp. HMWP2, Vibrio anguillarum AngR, and E. coliEntF. A mutant with an in-frame deletion of this gene, namedvibF, was created with classical V. choleraestrain O395 by in vivo marker exchange. In cross-feeding studies, this mutant was unable to synthesize ferric vibriobactin but was able to utilize exogenous siderophore. Complementation of the mutant with a cloned vibF fragment restored vibriobactin synthesis to normal. The expression of the vibF promoter was found to be negatively regulated by iron at the transcriptional level, under the control of the V. cholerae fur gene. Expression ofvibF was not autoregulatory and neither affected nor was affected by the expression of irgA or viuA. The promoter of vibF was located by primer extension and was found to contain a dyad symmetric nucleotide sequence highly homologous to the E. coli Fur binding consensus sequence. A footprint of purified V. cholerae Fur on the vibFpromoter, overlapping the Fur binding consensus sequence, was observed using DNase I footprinting. The protein product of vibF is homologous to the multifunctional nonribosomal protein synthetases and is necessary for the biosynthesis of vibriobactin.

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