Abstract：
:Protein binding specificities can be manipulated by redesigning contacts that already exist at an interface or by expanding the interface to allow interactions with residues adjacent to the original binding site. Previously, we developed a strategy, called AnchorDesign, for expanding interfaces around linear binding epitopes. The epitope is embedded in a loop of a scaffold protein, in our case a monobody, and then surrounding residues on the monobody are optimized for binding using directed evolution or computational design. Using this strategy, we have increased binding affinities by >100-fold, but we have not tested whether it can be used to control protein binding specificities. Here, we test whether AnchorDesign can be used to engineer a monobody that binds specifically to the mitogen-activated protein kinase (MAPK) p38α but not to the related MAPKs ERK2 and JNK. To anchor the binding interaction, we used a small (D) docking motif from the mitogen-activated protein kinase kinase (MAP2K) MKK6 that interacts with similar affinity with p38α and ERK2. Our hypothesis was that by embedding the motif in a larger protein that we could expand the interface and create contacts with residues that are not conserved between p38α and ERK2. Molecular modeling was used to inform insertion of the D motif into the monobody, and a combination of phage and yeast display were used to optimize the interface. Binding experiments demonstrate that the engineered monobody binds to the target surface on p38α and does not exhibit detectable binding to ERK2 or JNK.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Hussain M,Angus SP,Kuhlman Bdoi
10.1021/acs.biochem.8b00408subject
Has Abstractpub_date
2018-07-31 00:00:00pages
4526-4535issue
30eissn
0006-2960issn
1520-4995journal_volume
57pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:Telomeres terminate nearly exclusively in single-stranded DNA (ssDNA) overhangs comprised of the G-rich 3' end. This overhang varies widely in length from species to species, ranging from just a few bases to several hundred nucleotides. These overhangs are not merely a remnant of DNA replication but rather are the res...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.6b00496
更新日期：2016-09-27 00:00:00
abstract：:L-Aspartate oxidase (Laspo) catalyzes the conversion of L-Asp to iminoaspartate, the first step in the de novo biosynthesis of NAD(+). This bacterial pathway represents a potential drug target since it is absent in mammals. The Laspo R386L mutant was crystallized in the FAD-bound catalytically competent form and its t...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi015939r
更新日期：2002-03-05 00:00:00
abstract：:Two short amino acid motifs, WXGDXNXR and PXWCDRXL, define a large family of inositol polyphosphate 5-phosphatases. We tested the importance of seven of these conserved amino acids to substrate binding and catalysis by mutating each to alanine in the platelet 75 kDa inositol polyphosphate 5-phosphatase II (5-phosphata...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9602627
更新日期：1996-06-18 00:00:00
abstract：:Sequence-specific assignments of 1H NMR resonances are obtained for the backbone protons of Escherichia coli acyl carrier protein, acylated with an eight-carbon chain covalently attached to the prosthetic group thiol (octanoyl-ACP). Comparison of 1H-1H sequential connectivities in the NOESY spectra of octanoyl-ACP and...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00386a037
更新日期：1987-06-16 00:00:00
abstract：:Excitation energy transfer studies were carried out to determine the distance between the adenosinetriphosphatase (ATPase) site and a unique "fast-reacting" sulfhydryl (referred to as SH1) in myosin subfragment 1. The fluorescent moiety of the probe N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl)ethylene-diamine was used as th...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00520a035
更新日期：1981-08-18 00:00:00
abstract：:The phosphocarrier protein HPr of the phosphoenolpyruvate-dependent sugar transport system of Escherichia coli can exist in a phosphorylated and a nonphosphorylated form. During phosphorylation, the phosphoryl group is carried on a histidine residue, His15. The hydrogen-bonding state of this histidine was examined wit...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00487a026
更新日期：1990-09-04 00:00:00
abstract：:Genetic studies have previously demonstrated that the Saccharomyces cerevisiae CDC9 gene product, which is functionally homologous to mammalian DNA ligase I, is required for DNA replication and is also involved in DNA repair and genetic recombination. In the present study we have purified the yeast enzyme. When measur...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00162a013
更新日期：1992-12-01 00:00:00
abstract：:Class I major histocompatibility complex (MHC) proteins present peptide antigens to T cells during the immune response against viruses. Peptides are loaded into newly synthesized class I heterodimers in the endoplasmic reticulum such that most or all cell surface class I molecules contain peptides derived from endogen...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00192a020
更新日期：1994-07-05 00:00:00
abstract：:Messenger RNA degradation is an important component of overall gene expression. During the final step of eukaryotic mRNA degradation, exoribonuclease 1 (Xrn1) carries out 5' → 3' processive, hydrolytic degradation of RNA molecules using divalent metal ion catalysis. To initiate studies of the 5' → 3' RNA decay machine...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.9b01035
更新日期：2020-04-21 00:00:00
abstract：:Limited cleavages of human C1r by extrinsic proteases of various specificity (plasmin, elastase, chymotrypsin, thermolysin) yield dimeric associations of two globular domains, each comprised of the intact B chain disulfide linked to gamma, the C-terminal fragment of the A chain. These (gamma-B)2 domains, which are hom...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00366a029
更新日期：1986-09-09 00:00:00
abstract：:The Fo membrane domain of the F1Fo-ATP synthase complex has been purified from bovine heart mitochondria. The purification procedure involves the removal of peripheral membrane proteins, including F1-ATPase, from submitochondrial particles with guanidine hydrochloride, followed by extraction of Fo and other membrane p...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00191a026
更新日期：1994-06-28 00:00:00
abstract：:The binding of rabbit globin mRNA to the 25-kDa cap binding protein eIF-4E from human erythrocytes was found to be 5.3-fold stronger than the binding of the cap analogue m7GpppG to eIF-4E [Gross et al. (1990) Biochemistry 29, 5008-5012]. In order to investigate whether this effect is due to the longer sequence of nucl...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00120a020
更新日期：1992-02-11 00:00:00
abstract：:A nucleoside triphosphate binding site on calf thymus RNA polymerase II was identified by using photoaffinity analogues of adenosine 5'-triphosphate and guanosine 5'-triphosphate. Both radiolabeled 8-azidoadenosine 5'-triphosphate (8-N3ATP) and radiolabeled 8-azidoguanosine 5'-triphosphate (8-N3GTP) bound to a single ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00349a038
更新日期：1986-01-14 00:00:00
abstract：:Transition metal-transporting P1B-type CPx ATPases play crucial roles in mediating metal homeostasis and resistance in all cells. The degree to which N-terminal metal binding domains (MBDs) confer metal specificity to the transporter is unclear. We show that the two MBDs of the Zn/Cd/Pb effluxing pump Anabaena AztA ar...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi7006367
更新日期：2007-10-02 00:00:00
abstract：:We have studied the tridecadeoxynucleotide CGCGAATTACGCG (I), which contains an additional A at position 9 compared to the dodecanucleotide of which the crystal structure has been determined. Sequence I exhibits no distinct melting curve and also has a concentration-dependent pattern of peaks on reverse-phase chromato...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00371a025
更新日期：1986-11-18 00:00:00
abstract：:We assigned l-talarate dehydratase (TalrD) and galactarate dehydratase (GalrD) functions to a group of orthologous proteins in the mechanistically diverse enolase superfamily, focusing our characterization on the protein encoded by the Salmonella typhimurium LT2 genome (GI:16766982; STM3697). Like the homologous mande...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi7008882
更新日期：2007-08-21 00:00:00
abstract：:l-Aspartate oxidase, encoded by the nadB gene, is the first enzyme in the de novo synthesis of NAD+ in bacteria. This FAD-dependent enzyme catalyzes the oxidation of l-aspartate to generate iminoaspartate and reduced flavin. Distinct from most amino acid oxidases, it can use either molecular oxygen or fumarate to reox...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.7b00307
更新日期：2017-08-08 00:00:00
abstract：:Lactyl-CoA dehydratase consists of two enzymes, E1 and E2, and requires catalytic quantities of ATP for activity [Kuchta, R. D., & Abeles, R. H. (1985) J. Biol. Chem. 260, 13181-13189]. In contrast to E1, which contains no Fe, E2 contains 8.20 +/- 0.04 mol of Fe/mol of E2, one of which can be removed by 1,10-phenanthr...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00371a009
更新日期：1986-11-18 00:00:00
abstract：:Central to the pathology of Alzheimer's disease (AD) is the profuse accumulation of amyloid-beta (Abeta) peptides in the brain of affected individuals, and several amyloid precursor protein (APP) transgenic (Tg) mice models have been created to mimic Abeta deposition. Among these, the PDAPP Tg mice carrying the famili...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi051213+
更新日期：2005-10-25 00:00:00
abstract：:Introduction of specific structural probes into substrate binding sites of Escherichia coli glutamine synthetase is now possible. Various analogues of ATP substituted with an amino or sulfhydryl moiety at the 6- or 8-position of the purine ring have been found to substitute for ATP in the autoinactivation reaction of ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00349a020
更新日期：1986-01-14 00:00:00
abstract：:RNA competent in directing protein synthesis is sequestered in unfertilized sea urchin eggs as translationally quiescent, nonpolyribosomal, messenger ribonucleoprotein complexes (mRNPs). Following fertilization, these mRNPs are derepressed and actively translated, presumably due to changes in the mRNA-associated prote...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00553a029
更新日期：1980-06-10 00:00:00
abstract：:The association between the papillomavirus E1 and E2 proteins is an important regulatory interaction, imparting coordinated control of viral transcription and replication. Using fluorescence polarization, we have characterized the interactions between HPV-11 E1, HPV-11 E2, and DNA in solution at equilibrium. For these...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi982616v
更新日期：1999-04-06 00:00:00
abstract：:Using proton magnetic resonance, we have investigated imino and amino proton exchange in the Z form of the four oligomers d(Cbr8GCGCbr8G), d(CGm5CGCG), d(CG)6, and d(CG)12. In the latter two oligomers, all five exchangeable protons have been assigned. We find that proton acceptors such as NH3 or the basic form of Tris...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00472a008
更新日期：1990-05-22 00:00:00
abstract：:We found that peroxisomal lignoceroyl-CoA ligase, like palmitoyl-CoA ligase, is present in the peroxisomal membrane whereas the peroxisomal beta-oxidation enzyme system is localized in the matrix. To further define the role of peroxisomal acyl-CoA ligases (membrane component) in providing acyl-CoA for peroxisomal beta...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00468a027
更新日期：1990-04-24 00:00:00
abstract：:Epidermal growth factor receptor (EGFR) exemplifies the family of receptor tyrosine kinases that mediate numerous cellular processes, including growth, proliferation, and differentiation. Moreover, gene amplification and EGFR mutations have been identified in a number of human malignancies, making this receptor an imp...
journal_title：Biochemistry
pub_type： 杂志文章,评审
doi：10.1021/bi301441e
更新日期：2012-12-18 00:00:00
abstract：:Glutamate racemase, MurI, catalyzes the interconversion of glutamate enantiomers in a cofactor-independent fashion and provides bacteria with a source of D-Glu for use in peptidoglycan biosynthesis. The enzyme uses a "two-base" mechanism involving a deprotonation of the substrate at the alpha-position to form an anion...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi002703z
更新日期：2001-05-29 00:00:00
abstract：:M13 DNA containing 20-30 apurinic/apyrimidinic (AP) sites per intact circular molecule was prepared by growing phage on an ung- dut- Escherichia coli mutant and treating the DNA with uracil N-glycosylase. AP sites obstruct in vitro DNA synthesis catalyzed by E. coli pol I. The position at which termination of synthesi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00288a026
更新日期：1983-09-13 00:00:00
abstract：:Vanadium(IV) oxo-bis(maltolato) (BMOV), an organovanadium compound, is a potent insulinomimetic agent and improves glucose homeostasis in various models of diabetes. We have shown previously that BMOV stimulates the phosphorylation of PKB which may contribute as one of the mechanisms for the insulinomimetic effect of ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi060403x
更新日期：2006-09-26 00:00:00
abstract：:Stabilization of the plasma membrane Ca-ATPase (PMCA) in an inactive conformation upon oxidation of multiple methionines in the calcium regulatory protein calmodulin (CaM) is part of an adaptive cellular response to minimize ATP utilization and the generation of reactive oxygen species (ROS) under conditions of oxidat...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0474113
更新日期：2005-03-29 00:00:00
abstract：:The two dominant glucolipids in Acholeplasma laidlawii, viz., 1,2-diacyl-3-O-(alpha-D-glucopyranosyl)-sn-glycerol (MGlcDG) and 1,2-diacyl-3-O-[alpha-D-glucopyranosyl-(1----2)-O-alpha-D-glucopyranosyl ]- sn-glycerol (DGlcDG), have markedly different phase behavior. MGlcDG has an ability to form nonlamellar phases, wher...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00234a012
更新日期：1991-05-21 00:00:00
