RESUMO
Communicated by Ramaswamy H. Sarma.
Assuntos
DNA/química , DNA/metabolismo , Conformação de Ácido Nucleico , Fator de Transcrição TFIIIA/metabolismo , Animais , Modelos Moleculares , Ligação Proteica , Estrutura Secundária de Proteína , Xenopus laevisRESUMO
The mouse factor Zif268, known also as early growth response protein EGR-1, is a classical representative for the Cys2His2 transcription factor family. It is required for binding the RNA polymerase with operator dsDNA to initialize the transcription process. We have shown that only in this family of total six Zn-finger protein families the Zn complex plays a significant role in the protein-DNA binding. Electrostatic feature of this complex in the binding of factor Zif268 from Mus musculus with operator DNA has been considered. The factor consists of three similar Zn-finger units which bind with triplets of coding DNA. Essential contacts of the factor with the DNA phosphates are formed by three conservative His residues, one in each finger. We describe here the results of calculations of the electrostatic potentials for the Zn-Cys2His2 complex, Zn-finger unit 1, and the whole transcription factor. The potential of Zif268 has a positive area on the factor surface, and it corresponds exactly to the binding sites of each of Zn-finger units. The main part of these areas is determined by conservative His residues, which form contacts with the DNA phosphate groups. Our result shows that the electrostatic positive potential of this histidine residue is enhanced due to the Zn complex. The other contacts of the Zn-finger with DNA are related to nucleotide bases, and they are responsible for the sequence-specific binding with DNA. This result may be extended to all other members of the Cys2His2 transcription factor family.
Assuntos
DNA/química , Proteína 1 de Resposta de Crescimento Precoce/química , Histidina/química , Dedos de Zinco , Animais , Sítios de Ligação , DNA/metabolismo , DNA Ligases/química , DNA Ligases/genética , DNA Ligases/metabolismo , DNA Polimerase I/química , DNA Polimerase I/genética , DNA Polimerase I/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Proteína 1 de Resposta de Crescimento Precoce/genética , Proteína 1 de Resposta de Crescimento Precoce/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Histidina/metabolismo , Humanos , Camundongos , Proteínas de Manutenção de Minicromossomo/química , Proteínas de Manutenção de Minicromossomo/genética , Proteínas de Manutenção de Minicromossomo/metabolismo , Modelos Moleculares , Conformação de Ácido Nucleico , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Eletricidade Estática , Transcrição Gênica , Xenopus laevis/genética , Xenopus laevis/metabolismoRESUMO
ß-Hairpins are widespread in proteins, and it is possible to find them both within ß-sheets and separately. In this work, a comparative analysis of amino acid sequences of ß-strands within strongly twisted ß-hairpins from different structural protein subclasses has been conducted. Strongly twisted and coiled ß-hairpin generates in the space a right double helix out of ß-strands that are connected by a loop region (connections). The frequencies of amino acid residues on the internal (concave) and external (convex) surfaces of strongly twisted ß-hairpins have been determined (220 ß-hairpins from nonhomologous proteins were studied). The concave surface of these ß-hairpins is mainly generated by hydrophobic residues, while the convex surface by hydrophilic residues; accordingly, the alternation of hydrophobic internal and hydrophilic external residues is observed in their amino acid sequences. Amino acid residues of glycine and alanine (especially in places of the largest twisting of the strands) were anomalously frequently found in internal positions of strongly twisted and coiled ß-hairpins. It was established that internal positions never contain the proline residues, while external positions in the twisting region contain them in a relatively large amount. It was demonstrated that at least one amino acid residue in αL- or ε-conformation is required for generation of relatively short (up to 7 amino acid residues) connection. As a rule, these positions are occupied by glycines. Thus, not only the alternation of hydrophobic and hydrophilic amino acid residues, but also the presence of one or two glycine residues in the connection region and the excess of glycines and alanines in the places of the largest strand twisting on the concave surface, as well as the presence of prolines on the convex surface, are required to generate a strongly twisted and coiled ß-hairpin.
Assuntos
Proteínas/química , Sequência de Aminoácidos , Bases de Dados de Proteínas , Estrutura Secundária de Proteína , Proteínas/genéticaRESUMO
In the present study, two possible mechanisms of protein folding are analized. One of them is based on the hypothesis that at the first step of protein folding a nucleus is formed and then the remaining part of the molecule or domain is folded around it. For example, ß-proteins containing 3ß-corners can fold in this way. According to the other mechanism, the three-dimensional structure of proteins is formed as a result of interactions between "ready-made" building blocks. Analysis of structural features of the 3ß-corners and features of their amino asid sequences enable us to conclude that the 3ß-corner can fold into its unique structure per se and can act as a nucleus or "ready-made" building block in protein folding. The larger protein structures can be obtained by stepwise addition of ß-strands to the 3ß-corner in accordance with a restricted set of rules as shown in the corresponding structural tree, which is available at http://strees.protres.ru/. On the other hand, complementary interactions of the two 3ß-corners can result in formation of the fold that is observed in the serine protease domain and similar proteins.
Assuntos
Conformação Proteica , Dobramento de Proteína , Estrutura Secundária de Proteína , Serina Proteases/química , Aminoácidos/química , Aminoácidos/genética , Modelos Teóricos , Estrutura Terciária de Proteína , Alinhamento de SequênciaRESUMO
In the present study, pathways of growth of protein structures represented in the structural tree for ß-proteins containing 3ß-corners are analyzed. It is shown that the frequency of occurrence of the completed structures of known proteins within branches of the tree is quite different. This means that allowed pathways of growth of protein structures are not equal and their usage is quite different. In most cases, addition of one or two ß-strands nearest along the chain to the root 3ß-corner (67%) or addition of three ß-strands to the 3ß-corner results in the formation of structures closed into cycles or barrels. Therefore, the pathways that result in closed structures are used most often in the first steps of growth of the root 3ß-corner. Amino acid sequences coding for left-handed superhelices that close into cycles the 3ß-corners are also analyzed. It is demonstrated that most crossover sites where the polypeptide chain passes from one ß-layer to the other have one or two residues in sterically constrained α(L)- or ε-conformations, which should be glycines or residues with flexible side chains in order to reduce the steric constraints.