temporary banners

 



 

Journal Issue - Volume 17 Issue 12 (December 2008)

Abstract Serine proteases comprise nearly one‐third of all known proteases identified to date and play crucial roles in a wide variety of cellular as well as extracellular functions, including the process of blood clotting, protein digestion, cell signaling, inflammation, and protein processing. Their hallmark is that they contain the so‐called “classical” catalytic Ser/His/Asp triad. Although the classical serine proteases are the...

Abstract Structure is only the first step in understanding the interactions and functions of proteins. In this paper, we explore the flexibility of proteins across a broad database of over 250 solvated protein molecular dynamics simulations in water for an aggregate simulation time of ∼6 μs. These simulations are from our Dynameomics project, and these proteins represent approximately 75% of all known protein structures. We employ...

Abstract IκBα binds to and inhibits the transcriptional activity of NF‐κB family members via its ankyrin repeat (AR) domain. The binding affinity of IκBα with NF‐κB(p50/p65) heterodimers and NF‐κB(p65/65) homodimers is in the picomolar range, and in the cell, this results in long half‐lives of the complexes. Direct binding experiments have been performed using surface plasmon resonance (SPR) and isothermal titration calorimetry...

Abstract TREX1 is the major exonuclease in mammalian cells, exhibiting the highest level of activity with a 3′→5′ activity. This exonuclease is responsible in humans for Aicardi‐Goutières syndrome and for an autosomal dominant retinal vasculopathy with cerebral leukodystrophy. In addition, this enzyme is associated with systemic lupus erythematosus. TREX1 belongs to the exonuclease DEDDh family, whose members display low levels of...

Abstract Structural investigations are frequently hindered by difficulties in obtaining diffracting crystals of the target protein. Here, we report the crystallization and structure solution of the U2AF homology motif (UHM) domain of splicing factor Puf60 fused to Escherichia coli thioredoxin A. Both modules make extensive crystallographic contacts, contributing to a well‐defined crystal lattice with clear electron density for both...

Abstract In recent years, dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) has received considerable attention from a mechanistic and structural viewpoint. DHDPS catalyzes the reaction of (S)‐aspartate‐β‐semialdehyde with pyruvate, which is bound via a Schiff base to a conserved active‐site lysine (Lys161 in the enzyme from Escherichia coli). To probe the mechanism of DHDPS, we have studied the inhibition of E. coli DHDPS by the substrate...

Abstract During viral entry, HIV gp41 adopts a transient conformation called the “prehairpin intermediate” in which a highly conserved therapeutic target, the N‐trimer, is exposed. Despite extensive discovery efforts, potent and broadly neutralizing antibodies that target the N‐trimer are elusive. We previously demonstrated the N‐trimer is protected by a steric block that prevents large proteins, such as antibodies, from accessing...

Abstract Photoactive yellow protein (PYP), a blue‐light photoreceptor for Ectothiorhodospira halophila, has provided a unique system for studying protein folding that is coupled with a photocycle. Upon receptor activation by blue light, PYP proceeds through a photocycle that includes a partially folded signaling state. The last‐step photocycle is a thermal recovery reaction from the signaling state to the native state. Bi‐exponential kinetics...

Abstract Phosphorylase kinase (PhK) regulates glycogenolysis through its Ca2+‐dependent phosphorylation and activation of glycogen phosphorylase. The activity of PhK increases dramatically as the pH is raised from 6.8 to 8.2 (denoted as ↑pH), but Ca2+ dependence is retained. Little is known about the structural changes associated with PhK's activation by ↑pH and Ca2+, but activation by both mechanisms is mediated through regulatory subunits of the (αβγδ)4...

Abstract Biologically important human proteins often require mammalian cell expression for structural studies, presenting technical and economical problems in the production/purification processes. We introduce a novel affinity peptide tagging system that uses a low affinity anti‐peptide monoclonal antibody. Concatenation of the short recognition sequence enabled the successful engineering of an 18‐residue affinity tag with ideal...

Abstract The aggregation of antitrypsin into polymers is one of the causes of neonatal hepatitis, cirrhosis, and emphysema. A similar reaction resulting in disease can occur in other human serpins, and collectively they are known as the serpinopathies. One possible therapeutic strategy involves inhibiting the conformational changes involved in antitrypsin aggregation. The citrate ion has previously been shown to prevent antitrypsin...

Abstract S‐adenosylhomocysteine hydrolase (SAHH) is a ubiquitous enzyme that plays a central role in methylation‐based processes by maintaining the intracellular balance between S‐adenosylhomocysteine (SAH) and S‐adenosylmethionine. We report the first prokaryotic crystal structure of SAHH, from Mycobacterium tuberculosis (Mtb), in complex with adenosine (ADO) and nicotinamide adenine dinucleotide. Structures of complexes with three inhibitors...

Abstract Most synthetic inhibitors of peptidases have been targeted to the active site for inhibiting catalysis through reversible competition with the substrate or by covalent modification of catalytic groups. Cathepsin B is unique among the cysteine peptidase for the presence of a flexible segment, known as the occluding loop, which can block the primed subsites of the substrate binding cleft. With the occluding loop in the open...

Abstract Macromolecular crowding, a common phenomenon in the cellular environments, can significantly affect the thermodynamic and kinetic properties of proteins. A single‐molecule method based on atomic force microscopy (AFM) was used to investigate the effects of macromolecular crowding on the forces required to unfold individual protein molecules. It was found that the mechanical stability of ubiquitin molecules was enhanced by...

Abstract VirA, a secreted effector protein from Shigella sp., has been shown to be necessary for its virulence. It was also reported that VirA might be related to papain‐like cysteine proteases and cleave α‐tubulin, thus facilitating intracellular spreading. We have now determined the crystal structure of VirA at 3.0 Å resolution. The shape of the molecule resembles the letter “V,” with the residues in the N‐terminal third of the...

Page:   1 2 Next