Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies.

abstract：:Structural analysis of gelsolin domains 4-6 demonstrates that the two highest-affinity calcium ions that activate the molecule are in domains 5 and 6, one in each. An additional calcium site in domain 4 depends on subsequent actin binding and is seen only in the complex. The uncomplexed structure is primed to bind act...

journal_title：Journal of molecular biology

authors： Kolappan S,Gooch JT,Weeds AG,McLaughlin PJ

更新日期：2003-05-23 00:00:00

abstract：:The sequence RGITVNGKTYGR has been reported as part of a de novo design peptide system. This peptide folds as a beta-hairpin structure with three residues per strand and two residue turns. Asn6 side-chain, the residue in position L1 of the beta-turn, appeared to be solvent exposed, interacting only within the turn but...

journal_title：Journal of molecular biology

authors： Ramírez-Alvarado M,Blanco FJ,Niemann H,Serrano L

更新日期：1997-11-07 00:00:00

abstract：:The 8-17 deoxyribozyme is an in vitro selected enzyme capable of sequence-specific cleavage of RNA. While selected to be a magnesium and zinc-utilizing enzyme, the 8-17 DNAzyme has been shown to utilize lead for its catalysis. Fluorescence-based experiments have indicated that the magnesium- and zinc-utilizing version...

journal_title：Journal of molecular biology

authors： Liu Y,Sen D

更新日期：2010-01-15 00:00:00

abstract：:Phosphosignaling through pSer/pThr/pTyr is emerging as a common signaling mechanism in prokaryotes. The human pathogen Staphylococcus aureus produces two low-molecular-weight protein tyrosine phosphatases (PTPs), PtpA and PtpB, with unknown functions. To provide the structural context for understanding PtpA function a...

journal_title：Journal of molecular biology

authors： Vega C,Chou S,Engel K,Harrell ME,Rajagopal L,Grundner C

更新日期：2011-10-14 00:00:00

abstract：:FSHD region gene 1 (FRG1) is a dynamic nuclear and cytoplasmic protein that, in skeletal muscle, shows additional localization to the sarcomere. Maintaining appropriate levels of FRG1 protein is critical for muscular and vascular development in vertebrates; however, its precise molecular function is unknown. This stud...

journal_title：Journal of molecular biology

authors： Sun CY,van Koningsbruggen S,Long SW,Straasheijm K,Klooster R,Jones TI,Bellini M,Levesque L,Brieher WM,van der Maarel SM,Jones PL

更新日期：2011-08-12 00:00:00

abstract：:The type IC DNA methyltransferase M.EcoR124I is a trimeric enzyme of 162 kDa consisting of two modification subunits, HsdM, and a single specificity subunit, HsdS. Studies have been largely restricted to the HsdM subunit or to the intact methyltransferase since the HsdS subunit is insoluble when over-expressed indepen...

journal_title：Journal of molecular biology

authors： Smith MA,Read CM,Kneale GG

更新日期：2001-11-16 00:00:00

abstract：:Noncoding RNAs (ncRNAs), such as lncRNAs, circRNAs and pri-miRNAs, play important roles in physiological and pathological processes. Recently, it was demonstrated that they could encode proteins or peptides. However, relevant information is scattered across numerous published articles, which is inconvenient for the ex...

journal_title：Journal of molecular biology

authors： Liu H,Zhou X,Yuan M,Zhou S,Huang YE,Hou F,Song X,Wang L,Jiang W

更新日期：2020-05-15 00:00:00

abstract：:The adaptor protein Tks5/FISH (tyrosine kinase substrate 5/five SH3 domains, hereafter termed Tks5) is a crucial component of a protein network that controls the invasiveness of cancer cells and progression of Alzheimer's disease. Tks5 consists of an amino-terminal PX domain that is followed by five SH3 domains (SH3A-...

journal_title：Journal of molecular biology

authors： Rufer AC,Rumpf J,von Holleben M,Beer S,Rittinger K,Groemping Y

更新日期：2009-07-31 00:00:00

abstract：:We report the first protein phase-diagram characterized by a combination of volumetric, calorimetric, and spectroscopic techniques. More specifically, we use ultrasonic velocimetry, densimetry, and differential scanning calorimetry, in conjunction with UV absorbance and CD spectroscopy to detect and to characterize th...

journal_title：Journal of molecular biology

authors： Chalikian TV,Völker J,Anafi D,Breslauer KJ

更新日期：1997-11-28 00:00:00

abstract：:A homologue of the Escherichia coli GroEL apical domain was obtained from thermophilic eubacterium Thermus thermophilus. The domains share 70 % sequence identity (101 out of 145 residues). The thermal stability of the T. thermophilus apical domain (Tm>100 degrees C as evaluated by circular dichroism) is at least 35 de...

journal_title：Journal of molecular biology

authors： Hua Q,Dementieva IS,Walsh MA,Hallenga K,Weiss MA,Joachimiak A

更新日期：2001-02-23 00:00:00

abstract：:DNA structures bound to transcription factors are studied by using the crystal coordinates of complexes. Structural characteristics which are found at the sites where a protein secondary structure, an alpha-helix or a beta-sheet binds, can be understood in terms of fitting of the concave surface of the DNA major groov...

journal_title：Journal of molecular biology

authors： Suzuki M,Yagi N

更新日期：1996-02-09 00:00:00

abstract：:The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition sequence, cleaving both sites concertedly. While most restriction enzymes that act concurrently at two sites are tetramers, SgrAI is a dimer in solution. Its reaction at two cognate sites involves the association of two DNA-...

journal_title：Journal of molecular biology

authors： Wood KM,Daniels LE,Halford SE

更新日期：2005-07-08 00:00:00

abstract：:Crystal packing calculations have been carried out on a substantial number of conformations of Leu-enkephalin; namely, those obtained both from crystal structures and from energy minimizations on isolated molecules, and with and without waters of crystallization. The known crystal structures represent the most energet...

journal_title：Journal of molecular biology

authors： Glasser L,Scheraga HA

更新日期：1988-02-05 00:00:00

abstract：:The mitochondrial genome and the expression of the genes within it have evolved to be highly unusual in several lineages. Within alveolates, apicomplexans and dinoflagellates share the most reduced mitochondrial gene content on record, but differ from one another in organisation and function. To clarify how these char...

journal_title：Journal of molecular biology

authors： Slamovits CH,Saldarriaga JF,Larocque A,Keeling PJ

更新日期：2007-09-14 00:00:00

abstract：:An explanation is suggested for the roll alternation between low and high values in A-type nucleic acid duplexes containing alternating sequences of purine and pyrimidine residues. The explanation combines two points. (1) Roll inevitably occurs in A-type duplexes due to geometrical reasons. (2) Intrastrand base stacki...

journal_title：Journal of molecular biology

authors： Sponer J,Kypr J

更新日期：1991-10-05 00:00:00

abstract：:Methods for the prediction of protein function from structure are of growing importance in the age of structural genomics. Here, we focus on the problem of identifying sites of potential serine protease inhibitor interactions on the surface of proteins of known structure. Given that there is no sequence conservation w...

journal_title：Journal of molecular biology

authors： Jackson RM,Russell RB

更新日期：2000-02-18 00:00:00

abstract：:Mammalian lipoxygenases form a heterogeneous family of lipid peroxidizing enzymes, which have been implicated in synthesis of inflammatory mediators, in cell development and in the pathogenesis of various diseases (atherosclerosis, osteoporosis) with major health political importance. The crystal structures of two pla...

journal_title：Journal of molecular biology

authors： Hammel M,Walther M,Prassl R,Kuhn H

更新日期：2004-10-29 00:00:00

abstract：:Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl resi...

journal_title：Journal of molecular biology

authors： Mantri M,Krojer T,Bagg EA,Webby CJ,Butler DS,Kochan G,Kavanagh KL,Oppermann U,McDonough MA,Schofield CJ

更新日期：2010-08-13 00:00:00

abstract：:We report on the functional interplay between the His40, Glu58 and His92 catalysts of ribonuclease T1. The kinetic properties of the single His40Ala, Glu58Ala and His92Gln mutants have been compared with those of the corresponding double and triple mutants. When His40, Glu58 and His92 are mutated separately or togethe...

journal_title：Journal of molecular biology

authors： Steyaert J,Wyns L

更新日期：1993-02-05 00:00:00

abstract：:Arenaviruses are enveloped, negative-stranded RNA viruses that belong to the family Arenaviridae. This diverse family can be further classified into OW (Old World) and NW (New World) arenaviruses based on their antigenicity, phylogeny, and geographical distribution. Many of the NW arenaviruses are highly pathogenic vi...

journal_title：Journal of molecular biology

authors： Koma T,Huang C,Kolokoltsova OA,Brasier AR,Paessler S

更新日期：2013-12-13 00:00:00

abstract：:Crystallization of three different serine carboxypeptidases has been achieved by the method of hanging-drop vapor diffusion. Serine carboxypeptidases II from wheat bran and malted barley crystallize isomorphously from polyethylene glycol solutions at room temperature (pH 4 to 7) in space group P4(1)2(1)2 or enantiomor...

journal_title：Journal of molecular biology

authors： Wilson KP,Liao DI,Bullock T,Remington SJ,Breddam K

更新日期：1990-01-20 00:00:00

abstract：:Co-operativity in ATP hydrolysis by GroEL can be described by a model in which each ring of GroEL is in equilibrium between a low (T) and high (R) affinity state for ATP. According to this model, the GroEL double-ring is in equilibrium between three states: TT, TR and RR. In order to find out which states bind non-fol...

journal_title：Journal of molecular biology

authors： Yifrach O,Horovitz A

更新日期：1996-01-26 00:00:00

abstract：:A phylogenetically conserved ribosomal protein L16p/L10e organizes the architecture of the aminoacyl tRNA binding site on the large ribosomal subunit. Eukaryotic L10 also exhibits a variety of cellular activities, and, in particular, human L10 is known as a putative tumor suppressor, QM. We have determined the 2.5-A c...

journal_title：Journal of molecular biology

authors： Nishimura M,Kaminishi T,Takemoto C,Kawazoe M,Yoshida T,Tanaka A,Sugano S,Shirouzu M,Ohkubo T,Yokoyama S,Kobayashi Y

更新日期：2008-03-21 00:00:00

abstract：:The mobile element IS30 has dual target specificity, since it can integrate adjacent to the inverted repeat (IR) of another IS30 copy or into hot-spot sequences characterized by a well-defined consensus showing no similarity to the ends of the element. The result of such integrations into these targets is different, a...

journal_title：Journal of molecular biology

authors： Olasz F,Fischer T,Szabó M,Nagy Z,Kiss J

更新日期：2003-12-12 00:00:00

abstract：:Folding kinetics of large RNAs are just beginning to be investigated. We show that the Tetrahymena self-splicing RNA partitions into a population that rapidly reaches the native state, and a slowly folding population that is trapped in metastable misfolded structures. Transitions from the misfolded structures to the n...

journal_title：Journal of molecular biology

authors： Pan J,Thirumalai D,Woodson SA

更新日期：1997-10-17 00:00:00

abstract：:The Hippo pathway plays a crucial role in growth control, proliferation and tumor suppression. Activity of the signaling pathway is associated with cell density sensing and tissue organization. Furthermore, the Hippo pathway helps to coordinate cellular processes through crosstalk with growth-factor-mediated signaling...

journal_title：Journal of molecular biology

authors： Grannas K,Arngården L,Lönn P,Mazurkiewicz M,Blokzijl A,Zieba A,Söderberg O

更新日期：2015-10-23 00:00:00

abstract：:We improved a motility assay system by using an affinity-purified antibody against the C-terminal globular domain of characean myosin. This improvement allowed us to study the sensitivity to ionic strength or the processivity of characean myosin. The sliding velocity of actin filaments on a characean myosin-coated sur...

journal_title：Journal of molecular biology

authors： Awata JY,Kashiyama T,Ito K,Yamamoto K

更新日期：2003-02-21 00:00:00

abstract：:Association between the class II major histocompatibility complex (MHC) and the class II invariant chain-associated peptide (CLIP) occurs naturally as an intermediate step in the MHC class II processing pathway. Here, we report the crystal structure of the murine class II MHC molecule I-A(b) in complex with human CLIP...

journal_title：Journal of molecular biology

authors： Zhu Y,Rudensky AY,Corper AL,Teyton L,Wilson IA

更新日期：2003-02-28 00:00:00

abstract：:Elongation factor G (EF-G) is a large, five domain GTPase that catalyses the translocation of the tRNAs on the bacterial ribosome at the expense of GTP. In the crystal structure of GDP-bound EF-G, domain 1 (G domain) makes direct contacts with domains 2 and 5, whereas domain 4 protrudes from the body of the molecule. ...

journal_title：Journal of molecular biology

authors： Savelsbergh A,Matassova NB,Rodnina MV,Wintermeyer W

更新日期：2000-07-21 00:00:00

abstract：:We have developed an in vitro selection procedure to elucidate the specificity of RecA assisted oligonucleotide recognition of double stranded DNA. The procedure was based on formation of a synaptic complex between an oligonucleotide-RecA filament and a supercoiled plasmid bearing a homologous partially degenerate reg...

journal_title：Journal of molecular biology

authors： Malkov VA,Sastry L,Camerini-Otero RD

更新日期：1997-08-15 00:00:00