Increasing the thermostability of staphylococcal nuclease: implications for the origin of protein thermostability.

Abstract:

:Seven hyper-stable multiple mutants have been constructed in staphylococcal nuclease by various combinations of eight different stabilizing single mutants. The stabilities of these multiple mutants determined by guanidine hydrochloride denaturation were 3.4 to 5.6 kcal/mol higher than that of the wild-type. Their thermal denaturation midpoint temperatures were 12.6 to 22.9 deg. C higher than that of the wild-type. These are among the greatest increases in protein stability and thermal denaturation midpoint temperature relative to the wild-type yet attained. There has been great interest in understanding how proteins found in thermophilic organisms are stabilized. One frequently cited theory is that the packing of hydrophobic side-chains is improved in the cores of proteins isolated from thermophiles when compared to proteins from mesophiles. The crystal structures of four single and five multiple stabilizing mutants of staphylococcal nuclease were solved to high resolution. No large overall structural change was found, with most changes localized around the sites of mutation. Rearrangements were observed in the packing of side-chains in the major hydrophobic core, although none of the mutations was in the core. It is surprising that detailed structural analysis showed that packing had improved, with the volume of the mutant protein's hydrophobic cores decreasing as protein stability increased. Further, the number of van der Waals interactions in the entire protein showed an experimentally significant increase correlated with increasing stability. These results indicate that optimization of packing follows as a natural consequence of increased protein thermostability and that good packing is not necessarily the proximate cause of high stability. Another popular theory is that thermostable proteins have more electrostatic and hydrogen bonding interactions and these are responsible for the high stabilities. The mutants here show that increased numbers of electrostatic and hydrogen bonding interactions are not obligatory for large increases in protein stability.

journal_name

J Mol Biol

authors

Chen J,Lu Z,Sakon J,Stites WE

doi

10.1006/jmbi.2000.4140

keywords:

subject

Has Abstract

pub_date

2000-10-20 00:00:00

pages

125-30

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)94140-8

journal_volume

303

pub_type

杂志文章
  • Some motile properties of fast characean myosin.

    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

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01469-9

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

    更新日期:2003-02-21 00:00:00

  • Different subdomains are most protected from hydrogen exchange in the molten globule and native states of human alpha-lactalbumin.

    abstract::alpha-Lactalbumin (alpha-LA) is a two-domain, calcium-binding protein that forms one of the best studied molten globules. We present here amide hydrogen exchange studies of the molten globule formed by human alpha-LA at pH 2 and compare these results with a similar study of the native state at pH 6.3. The most persist...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0579

    authors: Schulman BA,Redfield C,Peng ZY,Dobson CM,Kim PS

    更新日期:1995-11-10 00:00:00

  • Plasminogen activator inhibitor-2 is highly tolerant to P8 residue substitution--implications for serpin mechanistic model and prediction of nsSNP activities.

    abstract::The serine protease inhibitor (serpin) superfamily is involved in a wide range of cellular processes including fibrinolysis, angiogenesis, apoptosis, inflammation, metastasis and viral pathogenesis. Here, we investigate the unique mousetrap inhibition mechanism of serpins through saturation mutagenesis of the P8 resid...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.09.008

    authors: Di Giusto DA,Sutherland AP,Jankova L,Harrop SJ,Curmi PM,King GC

    更新日期:2005-11-11 00:00:00

  • High-resolution crystal structures of trimeric and rod phycocyanin.

    abstract::The phycobilisome light-harvesting antenna in cyanobacteria and red algae is assembled from two substructures: a central core composed of allophycocyanin surrounded by rods that always contain phycocyanin (PC). Unpigmented proteins called linkers are also found within the rods and core. We present here two new structu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.10.036

    authors: David L,Marx A,Adir N

    更新日期:2011-01-07 00:00:00

  • Ketoconazole-induced conformational changes in the active site of cytochrome P450eryF.

    abstract::The azole-based P450 inhibitor ketoconazole is used to treat fungal infections and functions by blocking ergosterol biosynthesis in yeast. Ketoconazole binds to mammalian P450 enzymes and this can result in drug-drug interactions and lead to liver damage. To identify protein-drug interactions that contribute to bindin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4803

    authors: Cupp-Vickery JR,Garcia C,Hofacre A,McGee-Estrada K

    更新日期:2001-08-03 00:00:00

  • Crystal structure of a T cell receptor Valpha11 (AV11S5) domain: new canonical forms for the first and second complementarity determining regions.

    abstract::We describe the X-ray crystallographic structure of a murine T cell receptor (TCR) Valpha domain ("Valpha85.33"; AV11S5-AJ17) to 1.85 A resolution. The Valpha85.33 domain is derived from a TCR that recognizes a type II collagen peptide associated with the murine major histocompatibility complex (MHC) class II molecule...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4794

    authors: Machius M,Cianga P,Deisenhofer J,Ward ES

    更新日期:2001-07-20 00:00:00

  • Metal-dependent conformational changes in a recombinant vWF-A domain from human factor B: a solution study by circular dichroism, fourier transform infrared and (1)H NMR spectroscopy.

    abstract::Factor B is a key component of the alternative pathway of complement and is cleaved by factor D into the Ba and Bb fragments when complexed with the activated form of C3, namely C3b. The Bb fragment contains a von Willebrand factor type A (vWF-A) domain, which is composed of an open twisted almost-parallel beta-sheet ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3632

    authors: Hinshelwood J,Perkins SJ

    更新日期:2000-04-21 00:00:00

  • The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis.

    abstract::UMP kinase (UMPK), the enzyme responsible for microbial UMP phosphorylation, plays a key role in pyrimidine nucleotide biosynthesis, regulating this process via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). We present crystal stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.07.045

    authors: Marco-Marín C,Gil-Ortiz F,Rubio V

    更新日期:2005-09-16 00:00:00

  • Error rate and specificity of human and murine DNA polymerase eta.

    abstract::We describe here the error specificity of mammalian DNA polymerase eta (pol eta), an enzyme that performs translesion DNA synthesis and may participate in somatic hypermutation of immunoglobulin genes. Both mouse and human pol eta lack intrinsic proofreading exonuclease activity and both copy undamaged DNA inaccuratel...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4937

    authors: Matsuda T,Bebenek K,Masutani C,Rogozin IB,Hanaoka F,Kunkel TA

    更新日期:2001-09-14 00:00:00

  • Structural basis for the higher Ca(2+)-activation of the regulated actin-activated myosin ATPase observed with Dictyostelium/Tetrahymena actin chimeras.

    abstract::Replacement of residues 228-230 or 228-232 of subdomain 4 in Dictyostelium actin with the corresponding Tetrahymena sequence (QTA to KAY replacement: half chimera-1; QTAAS to KAYKE replacement: full chimera) leads to a higher Ca(2+)-activation of the regulated acto-myosin subfragment-1 ATPase activity. The ratio of AT...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3467

    authors: Matsuura Y,Stewart M,Kawamoto M,Kamiya N,Saeki K,Yasunaga T,Wakabayashi T

    更新日期:2000-02-18 00:00:00

  • Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase.

    abstract::DNA polymerases with intrinsic proofreading activity interact with DNA primer/templates in two distinct modes, corresponding to the complexes formed during the 5'-3' polymerization or 3'-5' editing of a nascent DNA chain. Thermodynamic measurements designed to quantify the energetic contributions of individual DNA-pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.11.023

    authors: Bailey MF,van der Schans EJ,Millar DP

    更新日期:2004-02-20 00:00:00

  • Topological frustration and the folding of interleukin-1 beta.

    abstract::The cytokine, interleukin-1beta (IL-1beta), adopts a beta-trefoil fold. It is known to be much slower folding than similarly sized proteins, despite having a low contact order. Proteins are sufficiently well designed that their folding is not dominated by local energetic traps. Therefore, protein models that encode on...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.11.074

    authors: Gosavi S,Chavez LL,Jennings PA,Onuchic JN

    更新日期:2006-03-31 00:00:00

  • LC3-Associated Phagocytosis and Inflammation.

    abstract::LC3-associated phagocytosis (LAP) is a novel form of non-canonical autophagy where LC3 (microtubule-associated protein 1A/1B-light chain 3) is conjugated to phagosome membranes using a portion of the canonical autophagy machinery. The impact of LAP to immune regulation is best characterized in professional phagocytes,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2017.08.012

    authors: Heckmann BL,Boada-Romero E,Cunha LD,Magne J,Green DR

    更新日期:2017-11-24 00:00:00

  • Solution structure of the RBCC/TRIM B-box1 domain of human MID1: B-box with a RING.

    abstract::B-box domains are a defining feature of the tripartite RBCC (RING, B-box, coiled-coil) or TRIM proteins, many of which are E3 ubiquitin ligases. However, little is known about the biological function of B-boxes. In some RBCC/TRIM proteins there is only a single B-box (type 2) domain, while others have both type 1 and ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.02.009

    authors: Massiah MA,Simmons BN,Short KM,Cox TC

    更新日期:2006-04-28 00:00:00

  • Ape1 abasic endonuclease activity is regulated by magnesium and potassium concentrations and is robust on alternative DNA structures.

    abstract::Abasic lesions are common mutagenic or cytotoxic DNA damages. Ape1 is the major human apurinic/apyrimidinic (AP) endonuclease and initiates repair of abasic sites by catalyzing strand cleavage at the lesion. I show here that Ape1 single-stranded (ss) AP site incision activity prefers 0.5 mM or 2 mM MgCl(2) and low con...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.11.028

    authors: Wilson DM 3rd

    更新日期:2005-02-04 00:00:00

  • Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.

    abstract::Many medically relevant Gram-negative bacteria use the type III secretion system (T3SS) to translocate effector proteins into the host for their invasion and intracellular survival. A multi-protein complex located at the cytosolic interface of the T3SS is proposed to act as a sorting platform by selecting and targetin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.07.004

    authors: Bernal I,Börnicke J,Heidemann J,Svergun D,Horstmann JA,Erhardt M,Tuukkanen A,Uetrecht C,Kolbe M

    更新日期:2019-09-06 00:00:00

  • Evolution of three human GPCRs for higher expression and stability.

    abstract::We recently developed a display method for the directed evolution of integral membrane proteins in the inner membrane of Escherichia coli for higher expression and stability. For the neurotensin receptor 1, a G-protein-coupled receptor (GPCR), we had evolved a mutant with a 10-fold increase in functional expression th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.02.051

    authors: Dodevski I,Plückthun A

    更新日期:2011-05-13 00:00:00

  • The SOCS box domain of SOCS3: structure and interaction with the elonginBC-cullin5 ubiquitin ligase.

    abstract::Suppressor of cytokine signalling 3 (SOCS3) is responsible for regulating the cellular response to a variety of cytokines, including interleukin 6 and leukaemia inhibitory factor. Identification of the SOCS box domain led to the hypothesis that SOCS3 can associate with functional E3 ubiquitin ligases and thereby induc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.06.038

    authors: Babon JJ,Sabo JK,Soetopo A,Yao S,Bailey MF,Zhang JG,Nicola NA,Norton RS

    更新日期:2008-09-12 00:00:00

  • The rabbit C family of short, interspersed repeats. Nucleotide sequence determination and transcriptional analysis.

    abstract::The C repeat family was first observed in the rabbit beta-like gene family. We have estimated the repetition frequency of the C repeats, determined the nucleotide sequence of three intact members and one truncated member, and have investigated the size, tissue specificity, and intracellular localization of C repeat tr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90379-6

    authors: Cheng JF,Printz R,Callaghan T,Shuey D,Hardison RC

    更新日期:1984-06-15 00:00:00

  • Non-proteolytic functions of calpain-3 in sarcoplasmic reticulum in skeletal muscles.

    abstract::Mutations in CAPN3/Capn3, which codes for skeletal muscle-specific calpain-3/p94 protease, are responsible for limb-girdle muscular dystrophy type 2A. Using "knock-in" (referred to as Capn3(CS/CS)) mice, in which the endogenous calpain-3 is replaced with a mutant calpain-3:C129S, which is a proteolytically inactive bu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.01.057

    authors: Ojima K,Ono Y,Ottenheijm C,Hata S,Suzuki H,Granzier H,Sorimachi H

    更新日期:2011-04-01 00:00:00

  • Flexible stoichiometry and asymmetry of the PIDDosome core complex by heteronuclear NMR spectroscopy and mass spectrometry.

    abstract::Homotypic death domain (DD)-DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing fi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.11.021

    authors: Nematollahi LA,Garza-Garcia A,Bechara C,Esposito D,Morgner N,Robinson CV,Driscoll PC

    更新日期:2015-02-27 00:00:00

  • Functional interactions between the subunits of the lactose transporter from Streptococcus thermophilus.

    abstract::Although the quaternary state has been assessed in detail for only a few members of the major facilitator superfamily (MFS), it is clear that multiple oligomeric states are represented within the MFS. One of its members, the lactose transporter LacS from Streptococcus thermophilus assumes a dimeric structure in the me...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.047

    authors: Geertsma ER,Duurkens RH,Poolman B

    更新日期:2005-07-01 00:00:00

  • Shape-specific nucleotide binding of single-stranded RNA by the GLD-1 STAR domain.

    abstract::Proteins containing the STAR RNA-binding domain fulfill vital roles in RNA biogenesis, yet a detailed understanding of STAR domain RNA binding specificity is lacking. In Caenorhabditis elegans, the STAR protein GLD-1 directly binds the 28 nucleotide recognition element TGE within the 3' untranslated region of tra-2 mR...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.11.049

    authors: Lehmann-Blount KA,Williamson JR

    更新日期:2005-02-11 00:00:00

  • Direct phage to intrabody screening (DPIS): demonstration by isolation of cytosolic intrabodies against the TES1 site of Epstein Barr virus latent membrane protein 1 (LMP1) that block NF-kappaB transactivation.

    abstract::The expression of intracellular antibodies (intrabodies) in eukaryotic cells has provided a powerful tool to manipulate microbial and cellular signaling pathways in a highly precise manner. However, there have been several technical issues that have restricted their more widespread use. In particular, single-chain ant...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.09.073

    authors: Gennari F,Mehta S,Wang Y,St Clair Tallarico A,Palu G,Marasco WA

    更新日期:2004-01-02 00:00:00

  • Mapping the Resistance Potential of Influenza's H+ Channel against an Antiviral Blocker.

    abstract::The development of drug resistance has long plagued our efforts to curtail viral infections in general and influenza in particular. The problem is particularly challenging since the exact mode of resistance may be difficult to predict, without waiting for untreatable strains to evolve. Herein, a different approach is ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.08.007

    authors: Assa D,Alhadeff R,Krugliak M,Arkin IT

    更新日期:2016-10-09 00:00:00

  • Cooperative effects of cofilin (ADF) on actin structure suggest allosteric mechanism of cofilin function.

    abstract::Using site-specific fluorescence probes and cross-linking we demonstrated that cofilin (ADF), a key regulator of actin cellular dynamics, weakens longitudinal contacts in F-actin in a cooperative manner. Differential scanning calorimetry detected a dual nature of cofilin effects on F-actin conformation. At sub-stoichi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.11.072

    authors: Bobkov AA,Muhlrad A,Pavlov DA,Kokabi K,Yilmaz A,Reisler E

    更新日期:2006-02-17 00:00:00

  • Principles governing amino acid composition of integral membrane proteins: application to topology prediction.

    abstract::A new method is suggested here for topology prediction of helical transmembrane proteins. The method is based on the hypothesis that the localizations of the transmembrane segments and the topology are determined by the difference in the amino acid distributions in various structural parts of these proteins rather tha...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2107

    authors: Tusnády GE,Simon I

    更新日期:1998-10-23 00:00:00

  • Defining the molecular basis of Arf and Hdm2 interactions.

    abstract::Understanding the interaction of Arf and Hdm2 has recently become a central issue in cancer biology. In response to hyperproliferative signals, p14(Arf) stabilizes p53 by binding to Hdm2 and inhibits the ubiquitination and subsequent proteosome-dependent degradation of p53. The medical importance of the Arf-Hdm2-p53 r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5110

    authors: Bothner B,Lewis WS,DiGiammarino EL,Weber JD,Bothner SJ,Kriwacki RW

    更新日期:2001-11-23 00:00:00

  • Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II.

    abstract::Human RNA polymerase II recognizes a strong transcriptional pause signal in the initially transcribed region of HIV-1. We report the use of a limited-step transcription assay to dissect the mechanism underlying recognition of and escape from this HIV-1 pause. Our results suggest that the primary determinant of transcr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4842

    authors: Palangat M,Landick R

    更新日期:2001-08-10 00:00:00

  • Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution.

    abstract::The X-ray crystal structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) and alpha-amylase 2 (TVAII) have been determined at 1.6 A and 2.3 A resolution, respectively. The structures of TVAI and TVAII have been refined, R-factor of 0.182 (R(free)=0.206) and 0.179 (0.224), respectively, with good chemical ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(02)00111-0

    authors: Kamitori S,Abe A,Ohtaki A,Kaji A,Tonozuka T,Sakano Y

    更新日期:2002-04-26 00:00:00