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Journal Issue - Volume 12 Issue 5 (May 2003)

Abstract ClpX requires ATP to unfold protein substrates and translocate them into the proteolytic chamber of ClpP for degradation. The steady‐state parameters for hydrolysis of ATP and ATPγS by ClpX were measured with different protein partners and the kinetics of degradation of ssrA‐tagged substrates were determined with both nucleotides. ClpX hydrolyzed ATPγS to ADP and thiophosphate at a rate (6/min) significantly slower than ATP...

Abstract We studied the non‐native aggregation of recombinant human granulocyte stimulating factor (rhGCSF) in solution conditions where native rhGCSF is both conformationally stable compared to its unfolded state and at concentrations well below its solubility limit. Aggregation of rhGCSF first involves the perturbation of its native structure to form a structurally expanded transition state, followed by assembly process to form an...

Abstract This study presents a site‐resolved experimental view of backbone CαH and NH internal motions in the 56‐residue immunoglobulin‐binding domain of streptococcal protein G, GB1. Using 13CαH and 15NH NMR relaxation data [T1, T2, and NOE] acquired at three resonance frequencies (1H frequencies of 500, 600, and 800 MHz), spectral density functions were calculated as F(ω) = 2ωJ(ω) to provide a model‐independent way to visualize and analyze internal motional...

Abstract In the present study, an attempt has been made to develop a method for predicting γ‐turns in proteins. First, we have implemented the commonly used statistical and machine‐learning techniques in the field of protein structure prediction, for the prediction of γ‐turns. All the methods have been trained and tested on a set of 320 nonhomologous protein chains by a fivefold cross‐validation technique. It has been observed that...

Abstract The hinge residues (Val29 and Ile36) of the switch I region (also known as the effector loop) of the Ha‐ras‐p21 protein have been mutated to glycines to accelerate the conformational changes typical for the effector loop. In this work, we have studied the influence of the combined mutations on the steady‐state structure of the switch I region of the protein in both the inactive GDP‐bound conformation as in the active GTP‐bound...

Abstract Protein disulfide isomerase (PDI, EC 5.3.4.1), an enzyme and chaperone, catalyses disulfide bond formation and rearrangements in protein folding. It is also a subunit in two proteins, the enzyme collagen prolyl 4‐hydroxylase and the microsomal triglyceride transfer protein. It consists of two catalytically active domains, a and a′, and two inactive ones, b and b′, all four domains having the thioredoxin fold. Domain b′ contains the...

Abstract Polyglutamine expansions, leading to aggregation, have been implicated in various neurodegenerative disorders. The range of repeats observed in normal individuals in most of these diseases is 19–36, whereas mutant proteins carry 40–81 repeats. In one such disorder, spinocerebellar ataxia (SCA1), it has been reported that certain individuals with expanded polyglutamine repeats in the disease range (Q12HQHQ12HQHQ14/15) but...

Abstract In protein structure prediction, it is often the case that a protein segment must be adjusted to connect two fixed segments. This occurs during loop structure prediction in homology modeling as well as in ab initio structure prediction. Several algorithms for this purpose are based on the inverse Jacobian of the distance constraints with respect to dihedral angle degrees of freedom. These algorithms are sometimes unstable...

Abstract Human T‐cell leukemia virus type 1 (HTLV‐I) is an oncogenic retrovirus that exhibits specific tropism for human T‐cells. The capsid (CA) proteins of retroviruses share highly conserved secondary and tertiary structures. However, they can form quaternary structures (assembled cores) that are conical (e.g., the lentivirus subgroup, including HIV) or spherical (e.g., the oncovirus subgroup, including HTLV). The intrinsic...

Abstract We report the effects of peptide binding on the 15N relaxation rates and chemical shifts of the C‐SH3 of Sem‐5. 15N spin‐lattice relaxation time (T1), spin‐spin relaxation time (T2), and {1H}‐15N NOE were obtained from heteronuclear 2D NMR experiments. These parameters were then analyzed using the Lipari‐Szabo model free formalism to obtain parameters that describe the internal motions of the protein. High‐order parameters (S2 > 0.8) are found...

Abstract α‐Hemolysin (αHL) is secreted by Staphylococcus aureus as a water‐soluble monomer that assembles into a heptamer to form a transmembrane pore on a target membrane. The crystal structures of the LukF water‐soluble monomer and the membrane‐bound α‐hemolysin heptamer show that large conformational changes occur during assembly. However, the mechanism of assembly and pore formation is still unclear, primarily because of the difficulty ...

Abstract In this paper we describe an improved neural network method to predict T‐cell class I epitopes. A novel input representation has been developed consisting of a combination of sparse encoding, Blosum encoding, and input derived from hidden Markov models. We demonstrate that the combination of several neural networks derived using different sequence‐encoding schemes has a performance superior to neural networks derived using...

Abstract The flavoenzyme DAAO from Rhodotorula gracilis, a structural paradigm of the glutathione‐reductase family of flavoproteins, is a stable homodimer with a flavin adenine dinucleotide (FAD) molecule tightly bound to each 40‐kD subunit. In this work, the thermal unfolding of dimeric DAAO was compared with that of two monomeric forms of the same protein: a Δloop mutant, in which 14 residues belonging to a loop connecting strands...

Abstract After a cytokine binds to its receptor on the cell surface (pH ∼7), the complex is internalized into acidic endosomal compartments (pH ∼5–6), where partially unfolded intermediates can form. The nature of these structural transitions was studied for wild‐type interleukin‐2 (IL‐2) and wild‐type granulocyte colony‐stimulating factor (G‐CSF). A noncoincidence of denaturation transitions in the secondary and tertiary structure...

Abstract Rat liver and Trypanosoma cruzi tyrosine aminotransferases (TATs) share over 40% sequence identity, but differ in their substrate specificities. To explore the molecular features related to these differences, comparative mutagenesis studies were conducted on full length T. cruzi TAT and N‐terminally truncated rat TAT recombinant enzymes. The functionality of Arg315 and Arg417 in rat TAT was investigated for comparison with the...

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