http://www.proteinscience.org Protein Science current issue RSS Feed http://www.proteinscience.org/details/journalArticle/411685/Multiple_diverse_ligands_binding_at_a_single_protein_site_A_matter_of_preexistin.html Abstract Here, we comment on the steadily increasing body of data showing that proteins with specificity actually bind ligands of diverse shapes, sizes, and composition. Such a phenomenon is not surprising when one considers that binding is a dynamic process with populations in equilibrium and that the shape of the binding site is strongly influenced by the molecular partner. It derives implicitly from the concept of populations.... 2009-01-01T00:00:00Z http://www.proteinscience.org/details/journalArticle/112942/Weak_alignment_offers_new_NMR_opportunities_to_study_protein_structure_and_dynam.html Abstract Protein solution nuclear magnetic resonance (NMR) can be conducted in a slightly anisotropic environment, where the orientational distribution of the proteins is no longer random. In such an environment, the large one‐bond internuclear dipolar interactions no longer average to zero and report on the average orientation of the corresponding vectors relative to the magnetic field. The desired very weak ordering, on the order... 2009-01-01T00:00:00Z http://www.proteinscience.org/details/journalArticle/112920/Low_free_energy_cost_of_very_long_loop_insertions_in_proteins.html Abstract Long insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded structure with amino‐ and carboxy‐termini in close proximity. A loop entropy reduction screen based on this concept was used in an attempt to retrieve folded sequences from random sequence libraries. A library of long random... 2009-01-01T00:00:00Z http://www.proteinscience.org/details/journalArticle/112130/Proteins_from_PHB_granules.html 2009-01-01T00:00:00Z http://www.proteinscience.org/details/journalArticle/112189/Detection_of_multiple_protein_conformations_by_laserpolarized_xenon.html 2009-01-01T00:00:00Z http://www.proteinscience.org/details/journalArticle/112160/Unfolding_of_Green_Fluorescent_Protein_mut2_in_wet_nanoporous_silica_gels.html Abstract Many of the effects exerted on protein structure, stability, and dynamics by molecular crowding and confinement in the cellular environment can be mimicked by encapsulation in polymeric matrices. We have compared the stability and unfolding kinetics of a highly fluorescent mutant of Green Fluorescent Protein, GFPmut2, in solution and in wet, nanoporous silica gels. In the absence of denaturant, encapsulation does not induce... 2009-01-01T00:00:00Z http://www.proteinscience.org/details/journalArticle/112220/Contributions_of_hydrophobic_domain_interface_interactions_to_the_folding_and_st.html Abstract Human γD‐crystallin (HγD‐Crys) is a monomeric eye lens protein composed of two highly homologous β‐sheet domains. The domains interact through interdomain side chain contacts forming two structurally distinct regions, a central hydrophobic cluster and peripheral residues. The hydrophobic cluster contains Met43, Phe56, and Ile81 from the N‐terminal domain (N‐td) and Val132, Leu145, and Val170 from the C‐terminal domain... 2009-01-01T00:00:00Z http://www.proteinscience.org/details/journalArticle/115105/The_1_9_A_crystal_structure_of_Escherichia_coli_MurG_a_membraneassociated_glycos.html Abstract The 1.9 Å X‐ray structure of a membrane‐associated glycosyltransferase involved in peptidoglycan biosynthesis is reported. This enzyme, MurG, contains two α/β open sheet domains separated by a deep cleft. Structural analysis suggests that the C‐terminal domain contains the UDP‐GlcNAc binding site while the N‐terminal domain contains the acceptor binding site and likely membrane association site. Combined with sequence data... 2008-12-31T00:00:00Z http://www.proteinscience.org/details/journalArticle/115127/Removal_of_the_Nterminal_hexapeptide_from_human_2microglobulin_facilitates_prote.html Abstract The solution structure and stability of N‐terminally truncated β2‐microglobulin (δN6β2‐m), the major modification in ex vivo fibrils, have been investigated by a variety of biophysical techniques. The results show that δN6β2‐m has a free energy of stabilization that is reduced by 2.5 kcal/mol compared to the intact protein. Hydrogen exchange of a mixture of the truncated and full‐length proteins at μM concentrations at pH... 2008-12-31T00:00:00Z http://www.proteinscience.org/details/journalArticle/115151/A_helixturn_motif_in_the_Cterminal_domain_of_histone_H1.html Abstract The structural study of peptides belonging to the terminal domains of histone H1 can be considered as a step toward the understanding of the function of H1 in chromatin. The conformational properties of the peptide Ac‐EPKRSVAFKKT KKEVKKVATPKK (CH‐1), which belongs to the C‐terminal domain of histone Hl° (residues 99–121) and is adjacent to the central globular domain of the protein, were examined by means of 1H‐NMR and... 2008-12-31T00:00:00Z http://www.proteinscience.org/details/journalArticle/115173/Detection_of_intact_megaDalton_protein_assemblies_of_vanillylalcohol_oxidase_by_.html Abstract Well‐resolved ion signals of intact large protein assemblies, with molecular masses extending above one million Dalton, have been detected and mass analyzed using electrospray ionization mass spectrometry, with an uncertainty in mass of <0.2%. the mass spectral data seem to reflect known solution‐phase behavior of the studied protein assembly and have therefore been directly used to probe the protein assembly topology... 2008-12-31T00:00:00Z http://www.proteinscience.org/details/journalArticle/115194/A_novel_method_of_affinitypurifying_proteins_using_a_bisarsenical_fluorescein.html Abstract Genetically‐encoded affinity tags constitute an important strategy for purifying proteins. Here, we have designed a novel affinity matrix based on the bis‐arsenical fluorescein dye FlAsH, which specifically recognizes short α‐helical peptides containing the sequence CCXXCC (Griffin BA, Adams SR, Tsien RY, 1998, Science 281:269–212). We find that kinesin tagged with this cysteine‐containing helix binds specifically to FlAsH resin and... 2008-12-31T00:00:00Z http://www.proteinscience.org/details/journalArticle/115245/Acetylcholinesterase_of_th_birthday.html Abstract Acetylcholinesterase (AChE) is an enzyme broadly distributed in many species, including parasites. It occurs in multiple molecular forms that differ in their quaternary structure and mode of anchoring to the cell surface. This review summarizes biochemical and immunological investigations carried out in our laboratories on AChE of the helmint, Schistosoma mansoni. AChE appears in S. mansoni in two principal molecular forms, both... 2008-12-31T00:00:00Z http://www.proteinscience.org/details/journalArticle/115219/Substrateassisted_catalysis_Molecular_basis_and_biological_significance.html Abstract Substrate‐assisted catalysis (SAC) is the process by which a functional group in a substrate contributes to catalysis by an enzyme. SAC has been demonstrated for representatives of three major enzyme classes: serine proteases, GTPases, and type II restriction endonucleases, as well as lysozyme and hexose‐1‐phosphate uridylyltransferase. Moreover, structure‐based predictions of SAC have been made for many additional enzymes.... 2008-12-31T00:00:00Z http://www.proteinscience.org/details/journalArticle/115275/The_interaction_of_neurotrophins_with_the_p75_NTR_common_neurotrophin_receptor_A.html Abstract Neurotrophins are a family of proteins with pleiotropic effects mediated by two distinct receptor types, namely the Trk family, and the common neurotrophin receptor p75NTR. Binding of four mammalian neurotrophins, nerve growth factor (NGF), brain‐derived neurotrophic factor (BDNF), neurotrophin‐3 (NT‐3), and neurotrophin‐4/5 (NT‐4/5), to p75NTR is studied by molecular modeling based on X‐ray structures of the neurotrophins and the... 2008-12-31T00:00:00Z