An iso-random Bi Bi mechanism has been proposed for adenylate kinase. In this mechanism, one of the enzyme forms can bind the substrates MgATP and AMP, whereas the other form can bind the products MgADP and ADP. In a catalytic cycle, the conformational changes of the free enzyme and the ternary complexes are the rate-limiting steps. The AP 5 A inhibition equations derived from this mechanism show theoretically that AP 5 A acts as a competitive inhibitor for the forward reaction and a mixed noncompetitive inhibitor for the backward reaction.

The time course of 8-anilino-1-naphthalenesulfonic acid (ANS) binding to adenylate kinase (AK) is a biphasic process. The burst phase ends in the dead-time of the stopped-flow apparatus (about 15 ms), whereas the slow phase completes in about 10 min. A Job's plot tests of the binding stoichiometry demonstrates that there is one ANS binding site on AK, but only about 70% of the enzyme can rapidly bind with ANS, indicating that the conformation of native AK molecules is not homogeneous. Further kinetic analysis shows that the effects of ANS and substrates concentration on the burst and slow phase fluorescence building agree well with the multiple native forms mechanism. One form (denoted N 1 ) binds with ANS, whereas the other (denoted N 2 ) does not. ANS binding to N 1 results in a burst phase fluorescence increase, followed by the interconversion of N 2 to N 1 , to give the slow phase ANS binding. Under urea denaturation conditions, N 2 is easily perturbed by urea and unfolds completely at low denaturant concentrations, whereas N 1 is relatively resistant to denaturation and unfolds at higher denaturant concentrations. The existence of multiple native forms in solution may shed some light on the interpretation of the enzyme catalytic mechanism.It has been accepted that a globular protein in its native state adopts a single, well defined conformation. However, this concept has been challenged by several reports that some proteins may exist in more than one distinct folded form in equilibrium. Evidence for distinguishing multiple native forms of staphylococcal nuclease has come from electrophoretic and NMR studies (1-6). For calbindin D 9K , evidence of multiple forms came not only from NMR studies, but also from x-ray crystal structure (7,8).Adenylate kinase (AK 1 ; EC 2.7.4.3) catalyzes the phosphoryl transfer reaction: MgATP ϩ AMP i MgADP ϩ ADP (9, 10). The enzyme contains two distinct nucleotide binding sites: the MgATP site, which binds MgATP and MgADP, and the AMP site, which is specific for AMP and uncomplexed ADP. The substrate-induced conformation changes in AK have been the subject of a number of investigations (11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22). Based on the comparison of AK crystal structures representing the enzyme in different ligand forms, apo-form (from pig muscle), enzyme-AMP binary complex (from beef heart mitochondrial matrix), and enzyme-AP 5 A complex (from Escherichia coli), Schulz and co-workers (15, 18) suggested that AK undergoes large structural changes upon substrates binding. These conformational changes can be subdivided into two steps; the first change, corresponding to binding to AMP, only involves the displacement of the small ␣-helical domain (residues 30 -59 in E. coli AK), whereas the second change, occurring with additional binding of substrate ATP, mainly involves the displacement of the LID domain (residues 122-159 in E. coli AK). However, it is not clear whether the enzyme achieves its catalytic conformation only upon substrate binding or whether the above confo...

The newly developed technique, electrospray mass spectrometry, was used to probe subtle conformational changes of bovine pancreatic RNase A during acid denaturation. In a dilute acid solution of pH 2.6, RNase A lost nearly all of its activity, whereas its intrinsic fluorescence intensity at 304 nm and its ellipticity at 222 nm were fairly resistant to denaturation by acetic acid. The observed maximum charged state of the enzyme in electrospray mass spectra was increased from 11 + (at pH 3.3) to 14 + (at pH 2.6). This could result from exposure of the buried basic amino acid residues R-10, K-41, 11-12 and perhaps H-48.

A truncated alkaline β-mannanase from alkaliphilic Bacillus sp. N16-5 (MAN330) was expressed and secreted in Kluyveromyces cicerisporus. The recombinant engineered strain for MAN330 production was stable during 80 generations, and the maximum yield of MAN330 reached 3,795 U/ml in 15 l fermenter. MAN330 exhibited similar pH optima, temperature optima, and substrate specificities to its full-length protein (MAN493). However, stability of MAN330 was about 7% higher than that of MAN493 from pH 9-11. MAN330 had about 10% higher stability than MAN493 from 60°C to 80°C.

BackgroundDNA damage response (DDR) plays pivotal roles in maintaining genome integrity and stability. An effective DDR requires the involvement of hundreds of genes that compose a complicated network. Because DDR is highly conserved in evolution, studies in lower eukaryotes can provide valuable information to elucidate the mechanism in higher organisms. Fission yeast (Schizosaccharomyces pombe) has emerged as an excellent model for DDR research in recent years. To identify novel genes involved in DDR, we screened a genome-wide S. pombe haploid deletion library against six different DNA damage reagents. The library covered 90.5% of the nonessential genes of S. pombe.ResultsWe have identified 52 genes that were actively involved in DDR. Among the 52 genes, 20 genes were linked to DDR for the first time. Flow cytometry analysis of the repair defective mutants revealed that most of them exhibited a defect in cell cycle progression, and some caused genome instability. Microarray analysis and genetic complementation assays were carried out to characterize 6 of the novel DDR genes in more detail. Data suggested that SPBC2A9.02 and SPAC27D7.08c were required for efficient DNA replication initiation because they interacted genetically with DNA replication initiation proteins Abp1 and Abp2. In addition, deletion of sgf73+, meu29+, sec65+ or pab1+ caused improper cytokinesis and DNA re-replication, which contributed to the diploidization in the mutants.ConclusionsA genome-wide screen of genes involved in DDR emphasized the key role of cell cycle control in the DDR network. Characterization of novel genes identified in the screen helps to elucidate the mechanism of the DDR network and provides valuable clues for understanding genome stability in higher eukaryotes.

In budding yeast and human cells, ING (inhibitor of growth) tumor suppressor proteins play important roles in response to DNA damage by modulating chromatin structure through collaborating with histone acetyltransferase or histone deacetylase complexes. However, the biological functions of ING family proteins in fission yeast are poorly defined. Here, we report that Png1p, a fission yeast ING homolog protein, is required for cell growth under normal and DNA-damaged conditions. Png1p was further confirmed to regulate histone H4 acetylation through collaboration with the MYST family histone acetyltransferase 1 (Mst1 The ING family members are well known candidate tumor growth suppressors (1). They are associated with certain areas of oncogenesis and cellular growth, such as cell cycle regulation, senescence, DNA damage repair, and apoptosis (2). Reduced mRNA expression, allelic loss, or somatic mutation of ING proteins were reported in many types of human cancers, including breast cancer, gastric cancer, melanoma, glioma, esophageal squamous cell carcinoma, and head and neck squamous cell carcinoma (2). However, the underlying mechanisms of ING proteins are still poorly understood.The DNA damage response process is very important for all living things to defeat the continuous threat of DNA damage caused by endogenous and exogenous factors and to maintain genome integrity (3). Chromosomal DNA in the eukaryotic nucleus is packaged into a very compact structure, and a critical step in DNA repair is to ensure that the DNA repair machinery can access the DNA. ING proteins always act as co-factors of histone acetyltransferases (HATs) 3 or histone deacetylases (HDACs) to acetylate or deacetylate the N-terminal tail of histone proteins (4, 5). This process can promote or inhibit access of DNA repair or gene transcription machinery to the DNA and is involved in DNA repair, gene transcription, and genome integrity (6, 7). Thus far, five human members (INGs1-5) and three budding yeast members (Yng1p, Yng2p, and Pho23p) have been characterized, and they all function with HATs or HDACs (8). Among these members, human ING3 is a stable component of the NuA4 HAT complex and functions in the DNA damage response pathway through regulation of histone H4/H2A acetylation or deacetylation (7, 9). The three budding yeast ING family proteins, Yng1p, Yng2p, and Pho23p, are subunits of the NuA3 HAT, NuA4 HAT, and Sin3/Rpd3 HDAC complexes, respectively. They regulate H3 acetylation, H4 acetylation, and histone deacetylation, respectively (10 -12). Each of these ING family proteins contain an N-terminal protein-protein interaction region, a nuclear localization signal, and a C-terminal plant homeodomain finger (1, 13). The most conserved motif, plant homeodomain, always functions as a histone code-signaling domain that recognizes the trimethylated lysine 4 residue of histone H3 (H3K4me3) to sense upstream signals (14 -17). However, the downstream pathway of histone code transduction by ING proteins still needs to be investigated.Fission yeas...

The fluorescence probe, 8-anilino-l-naphthalenesulfonic acid (ANS), was used to monitor the induced-fit conformational movement in rabbit muscle adenylate kinase. In 50 mM Tris-HCl buffer (pH 8.1), the time course of ANS binding to rabbit muscle adenylate kinase is a biphasic process. The fast phase completes within the dead-time of the stoppedflow equipment used (about 15 ms), while the slow phase ends in about 10 minutes. In the presence of 2.0 (iM peptidyl prolyl cisl rra/w-isomerase, the rate constant of the slow phase reaction is accelerated about 2.4-fold, suggesting that the domain movement during ANS binding to rabbit muscle adenylate kinase may involve proline isomerization. The activation energy of the slow phase was determined to be 74.6 kJ/mol, which is comparable to the activation energy of proline cis/frans-isomerization (about 80 kJ/mol).

There are two forms of rabbit muscle adenylate kinase (AK) with different 8-anilino-1-naphthalenesulfonic acid (ANS) binding properties in equilibrium solution. One form (about 70%, denoted N 1 ) binds rapidly with ANS, whereas the other (about 30%, denoted N 2 ) does not. Furthermore, native forms of AK should adopt different conformations for binding with substrates and products, which should be pre-existing for performing its catalytic function. The present experiments demonstrate both forms of AK distinguished by ANS probe are active. The activity of N 2 is about 0.8 fold higher than N 1 and shows higher susceptibility to proteolysis by trypsin. This means that the native state of AK might be an ensemble of kinetically attainable conformers and the energy landscapes of AK folding should be rugged with more than one local minimum. ß