121 results match your criteria glycines alanine


Why Are Gly31, Gly33, and Gly35 Highly Conserved in All Fluorescent Proteins?

Biochemistry 2021 12 22;60(49):3762-3770. Epub 2021 Nov 22.

Chemistry Department, Connecticut College, New London, Connecticut 06320, United States.

Green fluorescent protein (GFP)-like fluorescent proteins have been found in more than 120 species. Although the proteins have little sequence identity, Gly31, 33, and 35 are 87, 100, and 95% conserved across all species, respectively. All GFP-like proteins have a β-barrel structure composed of 11 β-sheets, and the 3 conserved glycines are located in the second β-sheet. Read More

View Article and Full-Text PDF
December 2021

Inward-facing glycine residues create sharp turns in β-barrel membrane proteins.

Biochim Biophys Acta Biomembr 2021 10 17;1863(10):183662. Epub 2021 Jun 17.

School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America. Electronic address:

The transmembrane region of outer-membrane proteins (OMPs) of Gram-negative bacteria are almost exclusively β-barrels composed of between 8 and 26 β-strands. To explore the relationship between β-barrel size and shape, we modeled and simulated engineered variants of the Escherichia coli protein OmpX with 8, 10, 12, 14, and 16 β-strands. We found that while smaller barrels maintained a roughly circular shape, the 16-stranded variant developed a flattened cross section. Read More

View Article and Full-Text PDF
October 2021

Combining targeted metabolite analyses and transcriptomics to reveal the specific chemical composition and associated genes in the incompatible soybean variety PI437654 infected with soybean cyst nematode HG1.2.3.5.7.

BMC Plant Biol 2021 May 14;21(1):217. Epub 2021 May 14.

State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.

Background: Soybean cyst nematode, Heterodera glycines, is one of the most devastating pathogens of soybean and causes severe annual yield losses worldwide. Different soybean varieties exhibit different responses to H. glycines infection at various levels, such as the genomic, transcriptional, proteomic and metabolomic levels. Read More

View Article and Full-Text PDF

Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water?

J Chem Theory Comput 2020 Jan 11;16(1):510-527. Epub 2019 Dec 11.

We examine the ability of six molecular dynamics (MD) force fields (Amber ff14SB, Amber ff99SBnmr1, Amber ff03ws, OPLS-AA/L, OPLS-AA/M, and CHARMM36) to reproduce conformational ensembles of the central alanine in GAG and AAA in a way that is consistent with five (GAG) or six (AAA) coupling constants and amide I' profiles. MD-derived Ramachandran plots for all six force fields under study differ from those obtained by the Gaussian fit to experimental data in three major ways: (i) the polyproline II (pPII) basin in the Ramachandran plot is too concentrated, (ii) the antiparallel β (aβ) basin is overpopulated, and (iii) the transitional β (βt) basin is underpopulated. Amber ff14SB outperforms the other five MD force fields and yields the highest pPII populations of the central alanine residue in GAG (55%) and AAA (63%), in good agreement with the predictions of the Gaussian model (59 and 76%). Read More

View Article and Full-Text PDF
January 2020

Conserved Glycines Control Disorder and Function in the Cold-Regulated Protein, COR15A.

Biomolecules 2019 03 2;9(3). Epub 2019 Mar 2.

Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.

Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly α-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Read More

View Article and Full-Text PDF

Glycine-rich loop encompassing active site at interface of hexameric M. tuberculosis Eis protein contributes to its structural stability and activity.

Int J Biol Macromol 2018 Apr 13;109:124-135. Epub 2017 Dec 13.

CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India. Electronic address:

RvEis is a crucial thermostable hexameric aminoglycoside acetyltransferase of Mycobacterium tuberculosis, overexpression of which confers Kanamycin resistance in clinical strains. The thermostability associated with hexameric RvEis is important for the enhanced intracellular survival of mycobacteria. However, the structural determinants responsible for its thermal stability remain unexplored. Read More

View Article and Full-Text PDF

Thiamethoxam Toxicity and Effects on Consumption Behavior in Orius insidiosus (Hemiptera: Anthocoridae) on Soybean.

Environ Entomol 2017 06;46(3):693-699

Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611

Neonicotinoid residues can be present in soybean vegetative tissue, prey insects, and flower tissues, possibly making them toxic to pollinators and natural enemies. Baseline information on the toxicity of neonicotinoids to beneficial insects other than pollinators through multiple routes of insecticide exposure is limited. The objectives of this study were 1) to evaluate the toxicity of thiamethoxam to the hemipteran predator, Orius insidiosus Say, exposed to residues through treated vegetative tissue and insect prey, and 2) to evaluate the effect of thiamethoxam on the abundance of this predator species in soybean fields. Read More

View Article and Full-Text PDF

Glycine Substitutions in Collagen Heterotrimers Alter Triple Helical Assembly.

Biomacromolecules 2017 02 18;18(2):617-624. Epub 2017 Jan 18.

Department of Chemistry, Rice University , 6100 Main Street, Houston, Texas 77005, United States.

Osteogenesis imperfecta typically results from missense mutations in the collagen genome where the required glycine residues are replaced with another amino acid. Many models have attempted to replicate the structure of mutated collagen on the triple helix level. However, composition and register control of the triple helix is complicated and requires extreme precision, especially when these destabilizing mutations are present. Read More

View Article and Full-Text PDF
February 2017

Experimental and Computational Analysis of Protein Stabilization by Gly-to-d-Ala Substitution: A Convolution of Native State and Unfolded State Effects.

J Am Chem Soc 2016 12 21;138(48):15682-15689. Epub 2016 Nov 21.

Department of Chemistry and ‡Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794-3400, United States.

The rational and predictable enhancement of protein stability is an important goal in protein design. Most efforts target the folded state, however stability is the free energy difference between the folded and unfolded states thus both are suitable targets. Strategies directed at the unfolded state usually seek to decrease chain entropy by introducing cross-links or by replacing glycines. Read More

View Article and Full-Text PDF
December 2016

[Relationship between structure and amino acid sequence of strongly twisted and coiled β-hairpins in globular proteins].

Mol Biol (Mosk) 2016 Sep-Oct;50(5):880-886

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.

β-Hairpins are widespread in proteins, and it is possible to find them both within β-sheets and separately. In this work, a comparative analysis of amino acid sequences of β-strands within strongly twisted β-hairpins from different structural protein subclasses has been conducted. Strongly twisted and coiled β-hairpin generates in the space a right double helix out of β-strands that are connected by a loop region (connections). Read More

View Article and Full-Text PDF

The impact of β-azido(or 1-piperidinyl)methylamino acids in position 2 or 3 on biological activity and conformation of dermorphin analogues.

J Pept Sci 2016 Aug;22(8):545-51

Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland.

The synthesis of new dermorphin analogues is described. The (R)-alanine or phenylalanine residues of natural dermorphin were substituted by the corresponding α-methyl-β-azidoalanine or α-benzyl-β-azido(1-piperidinyl)alanine residues. The potency and selectivity of the new analogues were evaluated by a competitive receptor binding assay in rat brain using [(3) H]DAMGO (a μ ligand) and [(3) H]DELT (a δ ligand). Read More

View Article and Full-Text PDF

Substrate determinants of signal peptide peptidase-like 2a (SPPL2a)-mediated intramembrane proteolysis of the invariant chain CD74.

Biochem J 2016 05 17;473(10):1405-22. Epub 2016 Mar 17.

Biochemical Institute, Christian Albrechts University of Kiel, Otto-Hahn-Platz 9, D-24118 Kiel, Germany

The presenilin homologue signal peptide peptidase-like 2a (SPPL2a) is an intramembrane protease of lysosomes/late endosomes which cleaves type II transmembrane proteins. We recently identified CD74, the invariant chain of the MHCII complex, as the first in vivo validated substrate of this protease. In endosomal compartments, CD74 undergoes sequential proteolysis leading to the generation of a membrane-bound N-terminal fragment (NTF) that requires cleavage by SPPL2a for its turnover. Read More

View Article and Full-Text PDF

Synthesis, Biological Activity, and NMR-Based Structural Studies of Deltorphin I Analogs Modified in Message Domain with a New α,α-Disubstituted Glycines.

Chem Biol Drug Des 2016 06 20;87(6):824-32. Epub 2016 Feb 20.

Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland.

This article describes new deltorphin I analogs in which phenylalanine residues were replaced by the corresponding (R) or (S)-α-benzyl-β-azidoalanine, α-benzyl-β-(1-pyrrolidinyl)alanine, α-benzyl-β-(1-piperidinyl)alanine, and α-benzyl-β-(4-morpholinyl)-alanine residues. The potency and selectivity of the new analogs were evaluated by a competitive receptor binding assay in the rat brain using [(3) H]DAMGO (a μ ligand) and [(3) H]DELT (a δ ligand). The affinity of analogs containing (R) or (S)-α-benzyl-β-azidoalanine in position 3 to δ-receptors strongly depended on the chirality of the α,α-disubstituted residue. Read More

View Article and Full-Text PDF

Self-Assembling Peptide Nanofiber Containing Long Motif of Laminin Induces Neural Differentiation, Tubulin Polymerization, and Neurogenesis: In Vitro, Ex Vivo, and In Vivo Studies.

Mol Neurobiol 2016 10 1;53(8):5288-99. Epub 2015 Oct 1.

Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, 1417755469, Iran.

Spinal cord injury (SCI) in humans stayed a ruining and healless disorder. Since longer laminin motif (CQAASIKVAV (CQIK)) better mimics conformation of native region in active site than isoleucine-lysine-valine-alanine-valine (IKVAV) and resulted in improved cellular response so, for the first time in this study, CQIK bounded with two glycines spacer and (RADA)4 as a self-assembling peptide nanofiber backbone (-CQIK) was used. The purpose of this study was to investigate the role of -CQIK in neural differentiation of human endometrial-derived stromal cells (hEnSCs) in vitro, tubulin polymerization ex vivo, and assess the supportive effect of this hydrogel in an animal model of chronic SCI. Read More

View Article and Full-Text PDF
October 2016

Biochemical characterization of the roles of glycines 24 and 27 and threonine 179 in tropomyosin from the fast skeletal trunk muscle of the atlantic salmon.

Biochemistry 2015 May 22;54(17):2769-76. Epub 2015 Apr 22.

Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada.

Atlantic salmon fast skeletal muscle is composed of an α-type tropomyosin that shares 20 substitutions with a mammalian homologue. Prominent isomorphisms considered to be potentially destabilizing include threonine 179 (core, Ala in rabbit) and a unique pair of glycines, residues 24 and 27. Bacterially expressed mutant tropomyosins were isolated without exposure to elevated temperature or organic solvent. Read More

View Article and Full-Text PDF

Analogues of deltorphin I containing conformationally restricted amino acids in position 2: structure and opioid activity.

J Pept Sci 2015 Feb 30;21(2):120-5. Epub 2014 Dec 30.

Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland.

New analogues of deltorphin I (DT I, Tyr-D-Ala-Phe-Asp-Val-Val-Gly-NH2 ), with the D-Ala residue in position 2 replaced by α-methyl-β-azido(amino, 1-pyrrolidinyl, 1-piperidinyl or 4-morpholinyl)alanine, were synthesized by a combination of solid-phase and solution methods. All ten new analogues were tested for receptor affinity and selectivity to μ- and δ-opioid receptors. The affinity of analogues containing (R) or (S)-α-methyl-β-azidoalanine in position 2 to δ-receptors strongly depended on the chirality of the α,α-disubstituted residue. Read More

View Article and Full-Text PDF
February 2015

Mechanical stability analysis of the protein L immunoglobulin-binding domain by full alanine screening using molecular dynamics simulations.

Biotechnol J 2015 Mar 16;10(3):386-94. Epub 2015 Jan 16.

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.

This article is the first to study the mechanical properties of the immunoglobulin-binding domain of protein L (referred to as protein L) and its mutants at the atomic level. In the structure of protein L, each amino acid residue (except for alanines and glycines) was replaced sequentially by alanine. Thus, 49 mutants of protein L were obtained. Read More

View Article and Full-Text PDF

Conformational and thermodynamic properties of non-canonical α,α-dialkyl glycines in the peptaibol Alamethicin: molecular dynamics studies.

J Phys Chem B 2014 Aug 12;118(33):9861-70. Epub 2014 Aug 12.

Departamento de Química, Escola de Ciências, Universidade do Minho , Largo do Paço, Braga 4704-553, Portugal.

In this work, we investigate the structure, dynamic and thermodynamic properties of noncanonical disubstituted amino acids (α,α-dialkyl glycines), also known as non-natural amino acids, in the peptaibol Alamethicin. The amino acids under study are Aib (α-amino isobutyric acid or α-methyl alanine), Deg (α,α-diethyl glycine), Dpg (α,α-dipropyl glycine), Dibg (α,α-di-isobutyl glycine), Dhg (α,α-dihexyl glycine), DΦg (α,α-diphenyl glycine), Dbzg (α,α-dibenzyl glycine), Ac6c (α,α-cyclohexyl glycine), and Dmg (α,α-dihydroxymethyl glycine). It is hypothesized that these amino acids are able to induce well-defined secondary structure in peptidomimetics. Read More

View Article and Full-Text PDF

Molecular modification of Protein A to improve the elution pH and alkali resistance in affinity chromatography.

Appl Biochem Biotechnol 2014 Apr 6;172(8):4002-12. Epub 2014 Mar 6.

The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China,

Protein A of Staphylococcus aureus has been widely used as an affinity ligand for the purification of immunoglobulin. However, the low elution pH and the sensitivity to alkaline condition restricted the large-scale application of antibody purification. To overcome these disadvantages, the B domain was selected and mutated to Z domain and the recombinant Protein A was reconstructed by linking five Z domains. Read More

View Article and Full-Text PDF

Identification of ligand specificity determinants in lantibiotic bovicin HJ50 and the receptor BovK, a multitransmembrane histidine kinase.

J Biol Chem 2014 Apr 13;289(14):9823-32. Epub 2014 Feb 13.

From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences and.

Lantibiotic bovicin HJ50 is produced by Streptococcus bovis HJ50 and acts as the extracellular signal to autoregulate its own biosynthesis through BovK/R two-component system. Bovicin HJ50 shows a linear N-terminal and glubolar C-terminal structure, and the sensor histidine kinase BovK contains eight transmembrane segments lacking any extensive surface-exposed sensory domain. The signal recognition mechanism between bovicin HJ50 and BovK is still unknown. Read More

View Article and Full-Text PDF

Functional asymmetry within the Sec61p translocon.

Proc Natl Acad Sci U S A 2013 Nov 4;110(47):18856-61. Epub 2013 Nov 4.

Biozentrum, University of Basel, CH-4056 Basel, Switzerland.

The Sec61 translocon forms a pore to translocate polypeptide sequences across the membrane and offers a lateral gate for membrane integration of hydrophobic (H) segments. A central constriction of six apolar residues has been shown to form a seal, but also to determine the hydrophobicity threshold for membrane integration: Mutation of these residues in yeast Sec61p to glycines, serines, aspartates, or lysines lowered the hydrophobicity required for integration; mutation to alanines increased it. Whereas four leucines distributed in an oligo-alanine H segment were sufficient for 50% integration, we now find four leucines in the N-terminal half of the H segment to produce significantly more integration than in the C-terminal half, suggesting functional asymmetry within the translocon. Read More

View Article and Full-Text PDF
November 2013

A conserved mechanism for gating in an ionotropic glutamate receptor.

J Biol Chem 2013 Jun 13;288(26):18842-52. Epub 2013 May 13.

Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania 17822-2621, USA.

Ionotropic glutamate receptor (iGluR) channels control synaptic activity. The crystallographic structure of GluA2, the prototypical iGluR, reveals a clamshell-like ligand-binding domain (LBD) that closes in the presence of glutamate to open a gate on the pore lining α-helix. How LBD closure leads to gate opening remains unclear. Read More

View Article and Full-Text PDF

Characterization of glycine substitution mutations within the putative NAD+-binding site of Bacillus licheniformis aldehyde dehydrogenase.

Protein Pept Lett 2012 Nov;19(11):1183-93

Department of Bioagricultural Science, National Chiayi University, Chiayi City 60004, Taiwan.

The NAD(+)-requiring enzymes of the aldehyde dehydrogenase (ALDH) family contain a glycine motif, GX1- 2GXXG, which is reminiscent of the fingerprint region of the Rossman fold, a conserved structural motif of the classical nicotinamide nucleotide-binding proteins. In this research, the role of three glycine residues situated within the putative NAD(+)-binding motif (211-GPGSSAG) together with Gly233 and Gly238 of Bacillus licheniformis ALDH (BlALDH) were probed by site-directed mutatgenesis. Fifteen mutant BlALDHs were obtained by substitution of the indicated glycine residues with alanine, glutamate and arginine. Read More

View Article and Full-Text PDF
November 2012

Role of a conserved glycine triplet in the NSS amino acid transporter KAAT1.

Biochim Biophys Acta 2012 Jul;1818(7):1737-44

Department of Molecular Sciences Applied to Biosystems, Universita degli Studi di Milano, Via Trentacoste 2, 20134 Milano, Italy.

K+-coupled amino acid transporter 1 (KAAT1) belongs to the NSS family of solute transporters and it is expressed in the midgut and in salivary glands of Manduca sexta larvae. As more than 80% of family members, KAATI shows a stretch of three glycines (G85-G87) that according to the structure of the prototype transporter LeuT, is located close to the access of the permeation pathway. In this work the role of the triplet has been investigated by alanine and cysteine scanning methods in protein heterologously expressed in Xenopus laevis oocytes. Read More

View Article and Full-Text PDF

The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ.

J Virol 2012 Apr 18;86(7):3605-16. Epub 2012 Jan 18.

Howard Hughes Medical Institute and the Department of Biochemistry & Biophysics, University of California at San Francisco, San Francisco, California, USA.

The activity of phosphatidylinositol 4-kinase class III beta (PI4KIIIβ) has been shown to be required for the replication of multiple picornaviruses; however, it is unclear whether a physical association between PI4KIIIβ and the viral replication machinery exists and, if it does, whether association is necessary. We examined the ability of the 3A protein from 18 different picornaviruses to form a complex with PI4KIIIβ by affinity purification of Strep-Tagged transiently transfected constructs followed by mass spectrometry and Western blotting for putative interacting targets. We found that the 3A proteins of Aichi virus, bovine kobuvirus, poliovirus, coxsackievirus B3, and human rhinovirus 14 all copurify with PI4KIIIβ. Read More

View Article and Full-Text PDF

Comprehensive solid-state NMR analysis reveals the effects of N-methylation on the molecular dynamics of glycine.

J Phys Chem B 2012 Jan 27;116(1):136-46. Epub 2011 Dec 27.

State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Wuhan, PR China.

Molecular dynamics of metabolites are important for their interactions and functions. To understand the structural dependence of molecular dynamics for N-methylated glycines, we comprehensively measured the (13)C and (1)H spin-lattice relaxation times for sarcosine, N,N-dimethylglycine, betaine, and betaine hydrochloride over a temperature range of 178-460 K. We found that the reorientations of methyl groups were observed for all these molecules, whereas reorientations of whole trimethylamine groups were detected in betaines. Read More

View Article and Full-Text PDF
January 2012

Conserved glycine residues in the P-loop of ATP synthases form a doorframe for nucleotide entrance.

J Mol Biol 2011 Oct 8;413(3):657-66. Epub 2011 Sep 8.

School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore.

The phosphate binding loop (GXXXXGKT(S)) is conserved in several mononucleotide-binding proteins with similar three-dimensional structures. Although variations in other amino acids have been noted, the first glycine and glycine-lysine residues are highly conserved in all enzymes, whose role is yet to be understood. Alanine substitutions for critically positioned glycines-G234, G237, and G239-were generated for the catalytic A-subunit of A-ATP synthase from Pyrococcus horikoshii OT3, and their crystal structures were determined. Read More

View Article and Full-Text PDF
October 2011

Functional impact of manipulation on the relative orientation of human prolactin receptor domains.

Biochemistry 2011 Jun 17;50(23):5333-44. Epub 2011 May 17.

Department of Veterinary Biosciences and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.

Hormone binding creates active receptor dimers for class 1 cytokine receptors; however, the detailed molecular mechanism by which these receptors are activated by their ligands is not well characterized, and it is unknown if these receptors share common mechanisms. A rotation model has been proposed for the activation of human erythropoietin receptor and human growth hormone receptor and is supported by evidence showing that additions of alanine at the junction of the transmembrane (TM) and intracellular (IC) domains and/or within the TM domain influenced receptor activities. This evidence suggests that alanine additions changed the relative orientations of the IC domains and their subsequent activation. Read More

View Article and Full-Text PDF

Modulatory ATP binding affinity in intermediate states of E2P dephosphorylation of sarcoplasmic reticulum Ca2+-ATPase.

J Biol Chem 2011 Apr 2;286(13):11792-802. Epub 2011 Feb 2.

Department of Physiology and Biophysics, Aarhus University, Aarhus C, Denmark.

The mechanism of ATP modulation of E2P dephosphorylation of sarcoplasmic reticulum Ca(2+)-ATPase wild type and mutant forms was examined in nucleotide binding studies of states analogous to the various intermediates of the dephosphorylation reaction, obtained by binding of metal fluorides, vanadate, or thapsigargin. Wild type Ca(2+)-ATPase displays an ATP affinity of 4 μM for the E2P ground state analog, 1 μM for the E2P transition state and product state analogs, and 11 μM for the E2 dephosphoenzyme. Hence, ATP binding stabilizes the transition and product states relative to the ground state, thereby explaining the accelerating effect of ATP on dephosphorylation. Read More

View Article and Full-Text PDF

Orientation and dynamics of synthetic transbilayer polypeptides containing GpATM dimerization motifs.

Biophys J 2011 Feb;100(3):656-664

Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada. Electronic address:

Deuterium NMR spectroscopy was used to study how the positioning of a dimerization motif within a transbilayer polypeptide influences its orientation and dynamics in bilayers. Three polypeptide variants comprising glycophorin A transmembrane (GpATM) dimerization motifs incorporated into lysine-terminated poly-leucine-alanine helices were mixed into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine multilamellar vesicles. The variants differed in orientation of the motif segment around the helix axis with respect to the peptide ends. Read More

View Article and Full-Text PDF
February 2011