... full-length
v-KIND; DKIND1, deletion of KIND1;
DKIND2, deletion of KIND2; DKIND1 + 2,
deletion of both KIND1 and KIND2; DRasN,
deletion of RasN; DGEF, deletion of
RasGEF; KIND1, KIND1 domain; KIND2,
KIND2 ... v-KIND KIND2 binding resides within
residues 702–744 of MAP2.
Residues 456–487 in the KIND2 domain of v-KIND
contain the core MAP2 binding module
To identify the core MAP2-binding site within ... sequence for v-KIND binding.
To evaluate the v-KIND KIND2-binding specificity
of residues 702–744 of MAP2, we performed a pull-
down assay of combinations of EGFP-fused KIND1
or KIND2 of v-KIND with...
... [238–240]. Even in the absence of pro-
tein–protein interactions, factors can assist each other’s
binding to DNA within nucleosomes. This principle is
illustrated in the model shown in Fig. 7A. In this ... considerable varia-
tion and complexity in the number of nucleosomes dis-
rupted, the histone composition of the remaining
nucleosomes, and the number andnatureof protein
complexes they interact with.
Much ... transcribed
regions of active genes in human T cells [124]. In a
study in yeast, mutations were introduced alone or in
combination in lysines 5, 8, 12 and 16 in the gene for
histone H4 [125]. Of these,...
... predicting,
measuring and understanding the roles of different kinds of organisms in the flux
and storage of elements in ecosystems. The total biomass per unit area, W,is
simply the sum ofthe ... size, in
comparison to a linear increase in gain as the driving force for the development
of gelatinous bodies. As seen above, however, the same principle of costs
increasing more rapidly than gains ... 28557 and Virginia Institute of
Marine Science, The College of William and
Mary, Gloucester Point, VA 23062.
Michael C. Marshall Department of
Zoology and Physiology, University of
Wyoming, Laramie,...
... (PX)
domain in the N-terminus. PX domains occur in a
variety of proteins involved in cell signaling, mem-
brane trafficking, and polarity establishment, and func-
tion as phosphoinositide-binding modules ... in the testis and fetal brain. The Noxo1c protein contains an
additional five amino acids in the N-terminal PX domain, a phosphoinosi-
tide-binding module; the domain plays an essential rolein ... domains with p22
phox
[25–
27]. Although the SH3 domain of Noxo1 participates in
regulation of Nox3, the roleof the PX domain in Nox3
activity remains unknown.
In the process of cloning of human...
... and C-terminal domain in red. (B) Ribbon representation of the structure of the PSI domain of barley prophytepsin [25] (N-terminal domain,
blue; C-terminal domain, red). (C) Model structure of ... family includes
saposins, which are lysosomal sphingolipid-activator pro-
teins [37], NK-lysin, granulysin, surfactant protein B,
amoebapores and domains of acid sphingomyelinase and
acyloxyacyl hydrolase ... folding, stability
and intracellular sorting of several zymogens [16], the PSI is
an insertion only identified in plant APs, which is highly
similar to saposins and saposin-like proteins and whose
biological...
... structure of
an ACh-binding protein reveals the ligand-binding domain of
nicotinic receptors. Nature 411, 269–276.
6. Dutertre,S.&Lewis,R.J.(2004)Computationalapproachesto
understand a-conotoxin interactions ... (Table 1). Interestingly, Vc1.1 was able to inhibit
in vivo a vascular response to pain and was effective in
alleviating chronic pain and accelerating functional recovery
in an animal model of neuropathy. ... transmembrane domain of each subunit contri-
butes to the formation of the hydrophilic pore. ACh binding protein
has structural and functional homology to the extracellular ligand
binding domain of the...
... freeze-intolerant insects
The structure andfunctionof b-helical antifreeze proteins
Steffen P. Graether and Brian D. Sykes
CIHR Group in Protein Structure and Function, Department of Biochemistry and Protein ... so, a considerable number of questions remain
before we can solve the interaction at the atomic level and
understand t he roleof the threonine side chains in ice
binding. The contradiction between ... f
isoform 337 with the structure o f th e l onger i soform CfAFP-501 using
the main chain of residues Thr23fiAsn90 in i soform 337 and residues
Thr54fiMet121 in CfAFP-501. (B) Overlap of isoforms...
... contained a 30 bp insertion in the
ORF, beginning at nucleotide 516. This resulted in
insertion of a 10 amino acid segment (TREIDYPETI)
and one substitution (Ser fi Gly) at the C-terminal
end of ... residue
cystine-knot domain. Injection of Spa
¨
tzle-C108, but not proSpa
¨
tzle-1A, into
larvae stimulated expression of several antimicrobial peptides and proteins,
including attacin-1, cecropin-6, moricin, lysozyme, ... development andin the antimicrobial immune response in larvae
and adults. We have investigated the functionof Spa
¨
tzle in a lepidopteran
insect, Manduca sexta, in which hemolymph proteinases activated...
... minidomain and the zinc-binding domain
of the zinc finger protein Ynr046w [25] (Fig. 8). The fit
of the heavy atoms (Ca, C, and N) from three
b-strands and the a-helices of both the closed and the
open ... specificity of the factor. The results provide new insights
into the possible roleof the C-domain in the process of translation termi-
nation.
Abbreviations
C-domain, C-terminal domain (or domain 3) of ... most of the residues of the protein rigid core
could be successfully fitted using models 1 and 2. For a few
residues of the minidomain (330–332, at the beginning of
the central b-strand) and residues...
... various organisms,
and the evolution of TLP and transthyretin.
The identification of TLPs and
transthyretins in nature
The evolution of transthyretin and its distribution in
nature have been well ... b-strands A, G and H [17].
Structural natureof the TLP and
transthyretin active sites
One of the striking features of transthyretin is the cen-
tral channel of the protein into which the THs bind.
This ... transthyretin dimers associate, via
nonpolar interactions, between the loops joining stands
G and H with the loops joining strands A and B, mak-
ing the transthyretin tetramer a ‘dimer of dimers.’
Recently,...
... FEBS
synthesis involving small modifying peptides (ubiquitin
and NEDD8) affecting protein stability. The most
intriguing recent finding is the phenotype resulting
from mutations in RPs in zebrafish, mice, and ... elusive. In Xenopus , two
proteins have been identified, La and cellular nucleic
acid-binding protein (CNBP) ⁄ zinc finger protein 9
(ZNF9), which bind the 5¢-UTRs of RP mRNAs in vitro.
La interacts ... mitogen-induced signal transduction path-
ways acting through TSC1–TSC2 and involving
mTORC1, as suggested by the rapamycin effect.
Rapamycin, which inhibits mTORC1 by binding to
mTOR in a complex...
... poly(C)-bind-
ing proteins: a multiplicity of functions and search for
mechanisms. RNA 8, 265–278.
32 Gamernik AV & Andino R (2000) Interactions of viral
protein 3CD and poly(rC) binding protein ... nucleotide at the 3¢-end of the ssDNA
strand (dC in 2AXY; dT in 2PQU) is participating in base-stacking interactions with the preceding cytosine base.
Structure andfunctionof KH domains R. Valverde ... sequences.
Although in both examples the coupling of two
RNA-binding domains will effectively increase the
specificity and affinity of the RNA–protein interaction,
the two different binding modes have...
... work and [36,37]). (f) It is proposed that the
FMN-a is bound to the inwards-pointing end of the
flavodoxin fold in the HoxY subunit. Such a flavodoxin fold
is conserved in the small subunit of all ... part that holds two of the Fe-S clusters in the small subunit of
the D. gigas enzyme is missing in HoxY of the SH, suggesting an
exposure of part of the hydrophobic surface of the HoxH subunit. ... used in all experiments. The
purity of the samples was examined by SDS/PAGE [29].
Protein concentrations were routinely determined by the
Bradford method [30] using bovine serum albumin as a
standard.
Activity...
... Irina Druzhinina
1
and Christian P. Kubicek
1
1
Division of Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Wien, Vienna;
2
Institute of Ecology,
University of ... significant differences in
amino acids flanking the active site. The 3D
model of Lad1 was fitted, according to the 2D
structure of SDH [25]. Amino acids involved
in binding of
D
-sorbitol [25] and conserved
between ... alignment of mammalian and fungal sorbitol dehydrogenases. Amino acids involved in binding of
D
-sorbitol [25] are marked by
asterisks, amino acids conserved between Lad1 and SDH in % are indicated...
... align-
ments of glucokinase and GlcNAc kinase and the common
ATP-binding domain, the GlcNAc kinase was fitted into the
glucokinase model using RasMol software. Figure 5 shows
the predicted structure of ... alignment of glucokinase and GlcNAc kinase. The amino acid sequences are numbered beginning with the first amino acid of the
N-terminus. Both amino acid sequences share the ATP binding subdomains (Phosphate1, ... for hexokinase
[30]. Binding of the sugar results in a strong conforma-
tional change allowing the binding of ATP. Mutations of
amino acids involved in this mechanism therefore result in
lower...