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PubMed2001

Structure of a variant of lac repressor with increased thermostability and decreased affinity for operator.

A single amino acid substitution, K84L, in the Escherichia coli lac repressor produces a protein that has substantially increased stability compared to wild-type. However, despite the increased stability, this altered tetrameric repressor has a tenfold reduced affinity for operator and greatly decreased rate-constants of inducer binding as well as a reduced phenotypic response to inducer in vivo. To understand the dramatic increase in stability and altered functional properties, we have determined the X-ray crystal structures of a dimeric repressor with and without the K84L substitution at resolutions of 1.7 and 3.0 A, respectively. In the wild-type dimer, K84-11, Lys84 forms electrostatic interactions at the monomer-monomer interface and is partially exposed to solvent. In the K84L-11 substituted protein there is reorientation of the N-subdomains, which allows the leucine to become deeply buried at the monomer-monomer interface. This reorientation of the N-subdomains, in turn, results in an alteration of hydrogen bonding, ion pairing, and van der Waals interactions at the monomer-monomer interface. The lysine residue at position 84 appears to exert its key effects by destabilizing the "optimal" conformation of the repressor, effectively loosening the dimer interface and allowing the repressor to adopt the conformations necessary to function as a molecular switch.

Amino Acid Substitution↗
PubMed1991

Structure of laminin variants. The 300-kDa chains of murine and bovine heart laminin are related to the human placenta merosin heavy chain and replace the a chain in some laminin variants.

A variant of laminin has previously been isolated from murine heart and shown to be distinct from laminin purified from a traditional source, the murine Engelbreth-Holm-Swarm (EHS) tumor (Paulsson, M., and Saladin, K. (1989) J. Biol. Chem. 264, 18726-18732). It contains a novel polypeptide chain designated as 300 kDa, which is not found in laminin from the EHS tumor. In the present study, heart laminin was purified from bovine tissue and shown to be structurally and immunochemically closely related to the murine protein. Further, heart laminins were compared with merosin, a laminin-like protein isolated from human placenta (Ehrig, K., Leivo, I., Argraves, W. S., Ruoslahti, E., and Engvall, E. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3264-3268). The 300-kDa chain of bovine heart laminin cross-reacted with the heavy chain of merosin, showing that these polypeptides are closely related, albeit from different species. Heart laminin is more resistant to proteolysis than laminin derived from the EHS tumor. A large fragment could be prepared by digestion with thermolysin, which consisted of an almost intact long arm structure and variably long, residual short arm structures. Analysis of its structure shows that the 300-kDa heavy chain is disulfide-bonded to the B1 and B2 chains in the center of the laminin cross and forms the long arm together with these chains. It thereby replaces the A chain, well known from tumor sources, in the laminin structure.

Amino Acid Sequence↗
PubMed2000

DNA breakage detection-FISH (DBD-FISH) in human spermatozoa: technical variants evidence different structural features.

Non-irradiated and X-irradiated (80 Gy) human spermatozoa were processed for in situ DNA breakage detection-FISH (DBD-FISH) of the whole genome, following two alternative variations of the basic technique. In the first, cells were initially incubated in the alkaline unwinding solution for transformation of DNA breaks into single-stranded DNA (ssDNA) to be hybridized, followed by the lysing solutions for protein removal. In the second, incubation in the lysing solutions was carried out before the denaturation step. The first approach yielded two subpopulations. While most sperm nuclei were faintly labeled and had chromocenters, a small subpopulation was strongly and homogeneously labeled, due to extensive DNA breakage. X-ray exposure increased the surface and mean fluorescence intensity. Otherwise, when the denaturation step was performed after protein extraction, all sperm nuclei yielded strong and dispersed FISH signals. Protein removal allows access of the unwinding solution to the DNA, which has abundant alkali-labile sites, and thus gives rise to large areas of ssDNA that are labeled by FISH. X-ray exposure increased the dispersion of FISH signals but decreased their mean fluorescence intensity. A linear dose-response was generated using the second experimental variant, being 30 Gy the lowest dose for detecting induction of damage by X-rays in mature sperm chromatin. These results indicate that DBD-FISH is not only useful for in situ detection of DNA breakage but also for revealing structural features of chromatin.

DNA↗
PubMed1997

Tissue-type plasminogen activator: variants and crystal/solution structures demarcate structural determinants of function.

NMR and crystal structure of many components of tissue-type plasminogen activator (t-PA) are now available: the finger-EGF pair and the kringle-2 domain structures have been solved, as have the proteolytic domains of vampire bat PA and human t-PA in two- and single-chain forms. These structures confirm the trypsin-like arrangement of the proteolytic domain of t-PA and show how surface loops near the catalytic centre contribute to the narrow specificity of t-PA. Together with mutational experiments, they identify the Lys156 sidechain as a cause of the amidolytic activity of single-chain t-PA, as it can provide a substitute salt bridge partner for Asp194 in the absence of the Ile16 N terminus of the two-chain form. These new findings provide new ideas for the design of PA variants with improved therapeutic properties.

Amino Acid Sequence↗
PubMed1979

[Different primary structure of 2 variants of Friend virus p 30 polypeptide separated by isoelectric focusing].

Variants of p 30 (iso-p 30s), the 30,000 dalton major polypeptide of murine C-type retraviruses, have been characterized in all virus strains by isoelectric focusing. Several of these iso-p 30s have been found to coexist in a given virus strain. In the present study, two iso-p 30s, characteristic of the Friend-Rauscher subgroup, separated by preparative isoelectric focusing of p 30 in thin layers of polydextran gel, were subjected to tryptic peptide mapping and aminoacid analysis. The two iso-p 30s, with isoelectric points (pI) of 6.5 and 7.1, were found to possess a partially different primary structure, with about 50% homology. The results are discussed.

Amino Acids↗
PubMed1980

Hemoglobin Legnano (alpha 2 141 (HC3) Arg leads to Leu beta2) a new high oxygen affinity variant. Functional and structural studies.

Hb Legnano (alpha 2 141 (HC3) Arg leads to Leu beta 2) is an abnormal hemoglobin, for which preliminary structural and functional studies demonstrated an amino acid substitution (Arg leads to Leu) in the alpha-C-terminus. This substitution modifies the functional properties observed in whole blood as well as in red blood cells, as reported in this paper. On the basis of its pI, previously determined by analytical isoelectric focusing (IEF), Hb Legnano was purified on a preparative IEF slab. The purified fraction was subjected to functional ultracentrifugal studies under various conditions of pH and salt concentration. The findings are compared with those for Hb Suresnes (alpha 2 141 (HC3) Arg leads His beta2) and Hb-CPB, a normal hemoglobin in which the C-terminal alpha 141 Arg has been cleaved by carboxypeptidase B. Hb Legnano, like the other hemoglobins considered, shows an increased P50, a decreased Hill's "n" values and a decreased Bohr effect that are partially restored in presence of organic phosphates. The presence of inorganic ions decreases the Bohr effect and enhances the dissociation into dimers, as observed in Hb-CPB. The dissociation of hemoglobin in carboxy form in ultracentrifugal studies and the different slope of Hill's "n" value as a function of pH are presumably due to presence of Leu, which probably modifies the stereochemistry of the variant.

Amino Acids↗
PubMed2006

Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation.

The green fluorescent protein (GFP) creates a fluorophore out of three sequential amino acids by promoting spontaneous posttranslational modifications. Here, we use high-resolution crystallography to characterize GFP variants that not only undergo peptide backbone cyclization but additional denaturation-induced peptide backbone fragmentation, native peptide hydrolysis, and decarboxylation reactions. Our analyses indicate that architectural features that favor GFP peptide cyclization also drive peptide hydrolysis. These results are relevant for the maturation pathways of GFP homologues, such as the kindling fluorescent protein and the Kaede protein, which use backbone cleavage to red-shift the spectral properties of their chromophores. We further propose a photochemical mechanism for the decarboxylation reaction, supporting a role for the GFP protein environment in facilitating radical formation and one-electron chemistry, which may be important in activating oxygen for the oxidation step of chromophore biosynthesis. Together, our results characterize GFP posttranslational modification chemistry with implications for the energetic landscape of backbone cyclization and subsequent reactions, and for the rational design of predetermined spontaneous backbone cyclization and cleavage reactions.

Crystallography, X-Ray↗
PubMed2004

New twists on H2A.Z: a histone variant with a controversial structural and functional past.

Integration of histone variants into chromatin organization allows for functional specification of chromatin regions. Recent functional analyses of H2A.Z have ascribed to it a multiplicity of complex and often opposing roles in developmental and homeostatic regulation. However, although the manner in which this essential histone variant is able to mediate its effects is not entirely well understood, current work has sought to investigate its mode of action. It is becoming increasingly clear that H2A.Z does not necessarily act independently, but rather, in conjunction with trans-acting factors to elicit chromatin changes. The nature of these structural changes has remained somewhat controversial but nevertheless exemplifies the seemingly multifaceted nature of H2A.Z.

Amino Acid Sequence↗
PubMed2001

Both normal and leukemic B lymphocytes express multiple isoforms of the human Aiolos gene.

Aiolos is a chromatin remodeling transcription regulator that plays an antiproliferative role in B lymphocyte function. In contrast to the related Ikaros factors, mammalian Aiolos has not been reported to generate splice variants. In addition, although human leukemic lymphoblasts express non-DNA-binding Ikaros isoforms with potential dominant negative effect on other interacting factors,the role of Aiolos in human lymphoid disorders has remained obscure. To address the question, why Aiolos should delineate from Ikaros in such a marked way, we have here analyzed whether also human Aiolos could generate alternate isoforms. According to the results obtained, both normal and neoplastic B lineage cells were found to express at least five novel Aiolos variants. Also structurally dominant negative variants with less than three DNA-binding domains were identified. In conclusion, given the multiplicity of also human Aiolos isoforms and thereby the evidently more intricate contribution of Aiolos to the chromatin remodeling machinery, it is suggested, that not only Ikaros, but also Aiolos could participate in a more versatile manner in the regulation of B lymphocyte function.

Alternative Splicing↗
PubMed2006

Relationship of catechol-O-methyltransferase variants to brain structure and function in a population at high risk of psychosis.

BACKGROUND: There is growing evidence that the gene catechol-O-methyltransferase (COMT) is involved in the etiopathogenesis of schizophrenia. This study sought to clarify the effects of the COMT Val158Met polymorphism on brain structure, function, and risk of developing schizophrenia in a well-characterized cohort of individuals at high risk of schizophrenia for familial reasons. METHODS: In a sample of 78 people at high genetic risk of schizophrenia, the risk of progression to schizophrenia associated with the COMT Val allele was estimated. The relationship of the Val allele to brain structure and function was investigated using structural magnetic resonance imaging (sMRI) and functional magnetic resonance imaging (fMRI) data collected on the high-risk subjects before their disease outcome was known. RESULTS: The COMT Val allele increased the risk of schizophrenia in this cohort in a dose-dependent manner. Subjects with the COMT Val allele had reduced gray matter density in anterior cingulate cortex. In addition, there was evidence of increased activation in lateral prefrontal cortex and anterior and posterior cingulated, with increasing sentence difficulty in those with the COMT Val allele despite a similar level of performance. CONCLUSIONS: The COMT Val allele is associated with an increased risk of schizophrenia in subjects at increased familial risk, in whom it has demonstrable effects on prefrontal brain structure and function. These patterns of altered brain structure and function have previously been associated with schizophrenia in this and other samples.

Adolescent↗
PubMed2005

Vaccines based on the native HIV Tat protein and on the combination of Tat and the structural HIV protein variant DeltaV2 Env.

The promising results obtained with the HIV-1 Tat-based vaccines in mice, monkeys and humans, a better understanding of Tat immunomodulatory functions, as well as evidence that vaccination with trimeric V2 loop-deleted HIV-1 Env induces cross-clade neutralizing antibodies led to the rational design of a novel vaccine based on the combination of Tat and V2-deleted Env.

AIDS Vaccines↗
PubMed2003

Structural and conformational variants of human beta2-microglobulin characterized by capillary electrophoresis and complementary separation methods.

The small (Mr = 11729) serum protein beta2-microglobulin is prone to precipitate as amyloid in a protein conformational disorder (PCD) that occurs in a significant number of patients on chronic hemodialysis. Analyses by capillary electrophoresis (CE) were undertaken to study beta2-microglobulin conformations under native separation conditions and showed an apparent heterogeneity of purified preparations when the sample matrix included organic solvents such as acetonitrile, trifluoroethanol and ethanol. We here present LC-MS, CE-MS, and CE studies of changes of separation profiles as a function of capillary temperature, organic solvent concentration, and analysis time. The results suggest that the apparent beta2-microglobulin heterogeneity observed by CE is caused by two distinct protein conformations that are present in beta2-microglobulin under partly denaturing conditions and that Met99-oxidized and normal (i.e. nonoxidized) beta2-microglobulin behave similarly with respect to the potential to attain this alternative conformation. CE is an attractive method to study early and intermediate soluble folding variants that may be involved in PCDs and CE thus may have an important role as a tool for understanding other PCDs characterized by amyloid deposition.

Electrophoresis, Capillary↗