The role of hydration in protein stability: comparison of the cold and heat unfolded states of Yfh1.

abstract：:The nine polyglutamine (polyQ) neurodegenerative diseases are caused in part by a gain-of-function mechanism involving protein misfolding, the deposition of β-sheet-rich aggregates and neuronal toxicity. While previous experimental evidence suggests that the polyQ-induced misfolding mechanism is context dependent, the...

journal_title：Journal of molecular biology

authors： Robertson AL,Bate MA,Buckle AM,Bottomley SP

更新日期：2011-11-04 00:00:00

abstract：:A 1.9 A resolution X-ray structure of the apo-form of Corynebacterium 2,5-diketo-d-gluconic acid reductase A (2,5-DKGR A), a member of the aldo-keto reductase superfamily, has been determined by molecular replacement using the NADPH-bound form of the same enzyme as the search model. 2,5-DKGR A catalyzes the NADPH-depe...

journal_title：Journal of molecular biology

authors： Sanli G,Blaber M

更新日期：2001-06-22 00:00:00

abstract：:As high-resolution cryogenic electron microscopy (cryo-EM) structures of ribosomes proliferate, at resolutions that allow atomic interactions to be visualized, this article attempts to give a perspective on the way research on ribosome structure and dynamics may be headed, and particularly the new opportunities we hav...

journal_title：Journal of molecular biology

authors： Frank J

更新日期：2016-09-11 00:00:00

abstract：:A dynamic structure refinement method for X-ray crystallography, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the low-frequency normal modes whose amplitudes and eigenvectors are experimentally optimized in the process of the crystallographic refinement. In th...

journal_title：Journal of molecular biology

authors： Kidera A,Go N

更新日期：1992-05-20 00:00:00

abstract：:The SH3 domain is a protein-protein interaction module commonly found in intracellular signaling and adaptor proteins. The SH3 domains of multiple endocytic proteins have been recently implicated in binding ubiquitin, which serves as a signal for diverse cellular processes including gene regulation, endosomal sorting,...

journal_title：Journal of molecular biology

authors： He Y,Hicke L,Radhakrishnan I

更新日期：2007-10-12 00:00:00

abstract：:Upon encounter with antigen, the B lymphocyte population responds by producing a diverse set of antigen-specific antibodies of various isotypes. The vast size of the responding populations makes it very difficult to study clonal evolution and repertoire composition occurring during these processes in humans. Here, we ...

journal_title：Journal of molecular biology

authors： Andréasson U,Flicker S,Lindstedt M,Valenta R,Greiff L,Korsgren M,Borrebaeck CA,Ohlin M

更新日期：2006-09-15 00:00:00

abstract：:The alcohol dehydrogenase (ADHase) enzyme catalyses the oxidation of alcohols to aldehydes or ketones using NAD+ as a cofactor. Functional ADHase from Drosophila lebanonensis is a dimer, with a monomeric molecular weight of 27,000 and with 254 residues in each polypeptide chain. Crystals of the protein have been grown...

journal_title：Journal of molecular biology

authors： Gordon EJ,Bury SM,Sawyer L,Atrian S,Gonzalez-Duarte R

更新日期：1992-09-05 00:00:00

abstract：:We report studies to determine which bacteriophage genes are required for assembly of phage HK97 proheads and what roles they play. We identify the gene encoding the major capsid protein of phage HK97 and report its DNA sequence, together with the DNA sequences of the two genes immediately upstream from it. When the c...

journal_title：Journal of molecular biology

authors： Duda RL,Martincic K,Hendrix RW

更新日期：1995-04-07 00:00:00

abstract：:One to four alanines were inserted by site-directed mutagenesis at three different locations within the alpha-helix comprising residues 39 to 50 in bacteriophage T4 lysozyme. All insertion mutants were correctly folded and catalytically active although the insertions led to a thermal destabilization by 1.1 to 4.2 kcal...

journal_title：Journal of molecular biology

authors： Heinz DW,Baase WA,Zhang XJ,Blaber M,Dahlquist FW,Matthews BW

更新日期：1994-02-25 00:00:00

abstract：:The eukaryotic 26S proteasome is a large multisubunit complex that degrades the majority of proteins in the cell under normal conditions. The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle and the 20S core particle. Most substrates are first covalently modified by ubiquitin, which the...

journal_title：Journal of molecular biology

authors： Budenholzer L,Cheng CL,Li Y,Hochstrasser M

更新日期：2017-11-10 00:00:00

abstract：:Allosteric communication between different subunits in metabolic enzyme complexes is of utmost physiological importance but only understood for few systems. We analyzed the structural basis of allostery in aminodeoxychorismate synthase (ADCS), which is a member of the family of glutamine amidotransferases and catalyze...

journal_title：Journal of molecular biology

authors： Semmelmann F,Straub K,Nazet J,Rajendran C,Merkl R,Sterner R

更新日期：2019-07-12 00:00:00

abstract：:The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has been refined at 2.14 A to a R-factor of 18.9%. The root-mean-square devi...

journal_title：Journal of molecular biology

authors： Tahirov TH,Lu TH,Liaw YC,Chen YL,Lin JY

更新日期：1995-07-14 00:00:00

abstract：:Single crystals of methanol dehydrogenase (MDH) from Methylobacterium extorquens AM1 have been grown by the vapour diffusion method. These crystals diffract to beyond 2 A resolution and are suitable for X-ray crystallography. They belong to the orthorhombic space group P2(1)2(1)2(1) and have the following unit cell pa...

journal_title：Journal of molecular biology

authors： Ghosh M,Harlos K,Blake CC,Richardson I,Anthony C

更新日期：1992-11-05 00:00:00

abstract：:The trimeric TolC protein of Escherichia coli comprises an outer membrane beta-barrel and a contiguous alpha-helical barrel projecting across the periplasm. This provides a single 140 A long pore for multidrug efflux and protein export. We have previously reported that trivalent cations such as hexammine cobalt can se...

journal_title：Journal of molecular biology

authors： Higgins MK,Eswaran J,Edwards P,Schertler GF,Hughes C,Koronakis V

更新日期：2004-09-17 00:00:00

abstract：:The free form of ribonuclease T1 (RNase T1) has been crystallized at neutral pH, and the three-dimensional structure of the enzyme has been determined at 1.5 A nominal resolution. Restrained least-squares refinement yielded an R value of 14.3% for 12,623 structure amplitudes. The high resolution of the structure analy...

journal_title：Journal of molecular biology

authors： Martinez-Oyanedel J,Choe HW,Heinemann U,Saenger W

更新日期：1991-11-20 00:00:00

abstract：:We have previously isolated sphericase (Sph), an extracellular mesophilic serine protease produced by Bacillus sphaericus. The Sph amino acid sequence is highly homologous to two cold-adapted subtilisins from Antarctic bacilli S39 and S41 (76% and 74% identity, respectively). Sph is calcium-dependent, 310 amino acid r...

journal_title：Journal of molecular biology

authors： Almog O,González A,Klein D,Greenblatt HM,Braun S,Shoham G

更新日期：2003-10-03 00:00:00

abstract：:We report a detailed all-atom simulation of the folding of the GCAA RNA tetraloop. The GCAA tetraloop motif is a very common and thermodynamically stable secondary structure in natural RNAs. We use our simulation methods to study the folding behavior of a 12-base GCAA tetraloop structure with a four-base helix adjacen...

journal_title：Journal of molecular biology

authors： Nivón LG,Shakhnovich EI

更新日期：2004-11-12 00:00:00

abstract：:Single crystals of ribonuclease I from Escherichia coli have been obtained by the vapor diffusion method. The crystals belong to the tetragonal space group P4(1)2(1)2 or its enantiomer P4(3)2(1)2 and have cell parameters a = b = 119.01 A and c = 34.40 A. There is one 27,000 dalton monomer in the asymmetric unit. The c...

journal_title：Journal of molecular biology

authors： Lim LW,Mathur S,Cannistraro VJ,Kennell D

更新日期：1993-11-20 00:00:00

abstract：:Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the pe...

journal_title：Journal of molecular biology

authors： Murina V,Kasari M,Takada H,Hinnu M,Saha CK,Grimshaw JW,Seki T,Reith M,Putrinš M,Tenson T,Strahl H,Hauryliuk V,Atkinson GC

更新日期：2019-08-23 00:00:00

abstract：:Integration host factor (IHF) of Escherichia coli is a histone-like protein that is involved both in site-specific recombination and in regulating the expression of a number of phage and bacterial genes. We have shown previously that transcription of the ilvGMEDA operon in E. coli is greatly reduced in IHF mutants. We...

journal_title：Journal of molecular biology

authors： Tsui P,Freundlich M

更新日期：1988-10-05 00:00:00

abstract：:Recent studies indicate that binding of the urokinase-type plasminogen activator (uPA) to its high-affinity receptor (uPAR) orchestrates uPAR interactions with other cellular components that play a pivotal role in diverse (patho-)physiological processes, including wound healing, angiogenesis, inflammation, and cancer ...

journal_title：Journal of molecular biology

authors： Barinka C,Parry G,Callahan J,Shaw DE,Kuo A,Bdeir K,Cines DB,Mazar A,Lubkowski J

更新日期：2006-10-20 00:00:00

abstract：:The Cip/Kip family of cyclin-dependent kinase (Cdk) inhibitors includes p21(Cip1), p27(Kip1) and p57(Kip2). Their kinase inhibitory activities are mediated by a homologous N-terminal kinase inhibitory domain. The Cdk inhibitory activity and stability of p27 have been shown to be regulated by a two-step phosphorylation...

journal_title：Journal of molecular biology

authors： Huang Y,Yoon MK,Otieno S,Lelli M,Kriwacki RW

更新日期：2015-01-30 00:00:00

abstract：:We use flexible backbone protein design to explore the sequence and structure neighborhoods of naturally occurring proteins. The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence...

journal_title：Journal of molecular biology

authors： Saunders CT,Baker D

更新日期：2005-02-18 00:00:00

abstract：:Bovine IF(1) is a basic, 84 amino acid residue protein that inhibits the hydrolytic action of the F(1)F(0) ATP synthase in mitochondria under anaerobic conditions. Its oligomerization state is dependent on pH. At a pH value below 6.5 it forms an active dimer. At higher pH values, two dimers associate to form an inacti...

journal_title：Journal of molecular biology

authors： Gordon-Smith DJ,Carbajo RJ,Yang JC,Videler H,Runswick MJ,Walker JE,Neuhaus D

更新日期：2001-04-27 00:00:00

abstract：:Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' pro...

journal_title：Journal of molecular biology

authors： Schierling K,Rösch S,Rupprecht R,Schiffer S,Marchfelder A

更新日期：2002-03-01 00:00:00

abstract：:Translation initiation of human Bip mRNA is directed by an internal ribosomal entry site (IRES) located in the 5' non-translated region. No trans-acting factor possibly involved in this process has as of yet been identified. For the encephalomyocarditis virus and other picornaviruses, polypyrimidine tract-binding prot...

journal_title：Journal of molecular biology

authors： Kim YK,Hahm B,Jang SK

更新日期：2000-11-24 00:00:00

abstract：:Bovine platelet factor 4 has been crystallized by "vapor dilution" in space group P2(1)2(1)2(1), a = 63.7 A, b = 66.7 A, c = 80.5 A, with four molecules, each 9505 Mr, in the asymmetric unit. The crystals diffract X-rays to better than 2.8 A resolution. ...

journal_title：Journal of molecular biology

authors： St Charles R,Ciaglowski RE,Walz D,Edwards BF

更新日期：1984-07-05 00:00:00

abstract：:The nuclear pore complex is the sole mediator of bidirectional transport between the nucleus and cytoplasm. Nup358 is a metazoan-specific nucleoporin that localizes to the cytoplasmic filaments and provides several binding sites for the mobile nucleocytoplasmic transport machinery. Here we present the crystal structur...

journal_title：Journal of molecular biology

authors： Lin DH,Zimmermann S,Stuwe T,Stuwe E,Hoelz A

更新日期：2013-04-26 00:00:00

abstract：:In eukaryotes, cellular levels of adenosine monophosphate (AMP) signal the metabolic state of the cell. AMP concentrations increase significantly upon metabolic stress, such as glucose deprivation in yeast. Here, we show that several DEAD-box RNA helicases are sensitive to AMP, which is not produced during ATP hydroly...

journal_title：Journal of molecular biology

authors： Putnam AA,Jankowsky E

更新日期：2013-10-23 00:00:00

abstract：:Recent computational studies of simple models of protein folding have concluded that a pronounced energy minimum (i.e. large gap in energy between low-energy states of the model) is a necessary and sufficient condition to ensure folding of a sequence to its lowest-energy conformation. Here, we show that this conclusio...

journal_title：Journal of molecular biology

authors： Unger R,Moult J

更新日期：1996-06-28 00:00:00