Folding of amphipathic alpha-helices on membranes: energetics of helix formation by melittin.

Abstract:

:Membranes have a potent ability to promote secondary structure formation in a wide range of membrane-active peptides, believed to be due to a reduction through hydrogen bonding of the energetic cost of partitioning peptide bonds. This process is of fundamental importance for understanding the mechanism of action of toxins and antimicrobial peptides and the stability of membrane proteins. A classic example of membrane-induced folding is the bee-venom peptide melittin that is largely unstructured when free in solution, but strongly adopts an amphipathic alpha-helical conformation when partitioned into membranes. We have determined the energetics of melittin helix formation through measurements of the partitioning free energies and the helicities of native melittin and of a diastereomeric analog with four d-amino acids (d4,l-melittin). Because D4,l-melittin has little secondary structure in either the free or bound forms, it serves as a model for the experimentally inaccessible unfolded bound form of native melittin. The partitioning of native melittin into large unilamellar phosphocholine vesicles is 5.0(+/-0.7) kcal mol-1 more favorable than the partitioning of d4,l-melittin (1 cal=4.186 J). Differences in the circular dichroism spectra of the two forms of melittin indicate that bound native melittin is more helical than bound d4, l-melittin by about 12 residues. These findings disclose that the free energy reduction per residue accompanying the folding of melittin in membrane interfaces is about 0.4 kcal mol-1, consistent with the hypothesis that hydrogen bonding reduces the high cost of partitioning peptide bonds. A value of 0.6 kcal mol-1 per residue has been observed for beta-sheet formation by a hexapeptide model system. These two values provide a useful rule of thumb for estimating the energetic consequences of membrane-induced secondary structure formation.

journal_name

J Mol Biol

authors

Ladokhin AS,White SH

doi

10.1006/jmbi.1998.2346

subject

Has Abstract

pub_date

1999-01-29 00:00:00

pages

1363-9

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(98)92346-4

journal_volume

285

pub_type

杂志文章
  • Molecular characterisation of aureocin A70, a multi-peptide bacteriocin isolated from Staphylococcus aureus.

    abstract::Staphylococcus aureus A70 produces a heat-stable bacteriocin designated aureocin A70. Aureocin A70 is encoded within a mobilisable 8 kb plasmid, pRJ6, and is active against Listeria monocytogenes. Experiments of transposition mutagenesis and gene cloning had shown that aureocin A70 production and immunity were associa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4885

    authors: Netz DJ,Sahl HG,Marcelino R,dos Santos Nascimento J,de Oliveira SS,Soares MB,do Carmo de Freire Bastos M

    更新日期:2001-08-31 00:00:00

  • Different binding modes of free and carrier-protein-coupled nicotine in a human monoclonal antibody.

    abstract::Nicotine is the principal addictive component of tobacco. Blocking its passage from the lung to the brain with nicotine-specific antibodies is a promising approach for the treatment of smoking addiction. We have determined the crystal structure of nicotine bound to the Fab fragment of a fully human monoclonal antibody...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.10.042

    authors: Tars K,Kotelovica S,Lipowsky G,Bauer M,Beerli RR,Bachmann MF,Maurer P

    更新日期:2012-01-06 00:00:00

  • Regulation and targeted mutation of opsA, coding for the NOP-1 opsin orthologue in Fusarium fujikuroi.

    abstract::Opsins are widespread photoreceptor proteins involved in a diversity of light-driven processes in all major taxa that use the apocarotenoid retinal as a light-absorbing prosthetic group. Proteins from the opsin family are also found in filamentous fungi, but no function has been attributed to them. The fungus Fusarium...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.01.057

    authors: Estrada AF,Avalos J

    更新日期:2009-03-20 00:00:00

  • Ligand binding energy and enzyme efficiency from reductions in protein dynamics.

    abstract::Tetrameric rabbit muscle glyceraldehyde 3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12) binds successively four molecules of its cofactor (NAD+) with affinities of ca 10(11) M(-1), 10(9) M(-1), 10(7) M(-1), and 10(5) M(-1). The reduction in the dynamics of the protein is greatest upon binding the first NAD+ molecule. S...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.11.015

    authors: Williams DH,Zhou M,Stephens E

    更新日期:2006-01-27 00:00:00

  • Molecular dynamics of native protein. I. Computer simulation of trajectories.

    abstract::The motion of the atoms in the small protein bovine pancreatic trypsin inhibitor has been simulated for about 60 picoseconds using two different potential energy functions. In one known as HHL the hydrogen bond is purely electrostatic, in the other, known as L79, the hydrogen bond is a directional O . . . H interactio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80304-0

    authors: Levitt M

    更新日期:1983-08-15 00:00:00

  • Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif.

    abstract::Many viruses employ ATP-powered motors for genome packaging. We combined genetic, biochemical, and single-molecule techniques to confirm the predicted Walker-B ATP-binding motif in the phage λ motor and to investigate the roles of the conserved residues. Most changes of the conserved hydrophobic residues resulted in >...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.08.012

    authors: delToro D,Ortiz D,Ordyan M,Pajak J,Sippy J,Catala A,Oh CS,Vu A,Arya G,Smith DE,Catalano CE,Feiss M

    更新日期:2019-11-08 00:00:00

  • Symmetry and chirality in topoisomerase II-DNA crossover recognition.

    abstract::Several experimental data support the notion that the recognition of DNA crossovers play an important role in the multiple functions of topoisomerase II. Here, a theoretical analysis of the possible modes of assembly of yeast topoisomerase II with right and left-handed tight DNA crossovers is performed, using the crys...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,meta分析

    doi:10.1006/jmbi.1998.2281

    authors: Timsit Y,Duplantier B,Jannink G,Sikorav JL

    更新日期:1998-12-18 00:00:00

  • DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli.

    abstract::It is becoming increasingly clear that the intrinsic and protein-induced topological properties of the DNA helix influence transcriptional efficiency. In this report we describe the properties of two upstream activating regions that influence transcription from the non-overlapping tandem promoters of the ilvGMEDA oper...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90460-2

    authors: Pagel JM,Winkelman JW,Adams CW,Hatfield GW

    更新日期:1992-04-20 00:00:00

  • Structure of the HIV-1 full-length capsid protein in a conformationally trapped unassembled state induced by small-molecule binding.

    abstract::The capsid (CA) protein plays crucial roles in HIV infection and replication, essential to viral maturation. The absence of high-resolution structural data on unassembled CA hinders the development of antivirals effective in inhibiting assembly. Unlike enzymes that have targetable, functional substrate-binding sites, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.11.027

    authors: Du S,Betts L,Yang R,Shi H,Concel J,Ahn J,Aiken C,Zhang P,Yeh JI

    更新日期:2011-02-25 00:00:00

  • Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change.

    abstract::The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. I...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.08.045

    authors: Crozier PS,Stevens MJ,Forrest LR,Woolf TB

    更新日期:2003-10-24 00:00:00

  • A New Type of Circular RNA derived from Nonconventional Introns in Nuclear Genes of Euglenids.

    abstract::Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.166758

    authors: Gumińska N,Zakryś B,Milanowski R

    更新日期:2021-02-05 00:00:00

  • One is Nothing without the Other: Theoretical and Empirical Analysis of Cell Growth and Cell Cycle Progression.

    abstract::Small, fast-growing bacteria make ideal subjects for genetic and quantitative analysis alike. Long the darling of theoreticians, efforts to understand the relationship between cell growth and cell cycle progression in bacterial systems have been propelled by modelers and empiricist in equal measure. Taking a historica...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2019.04.004

    authors: Levin PA,Taheri-Araghi S

    更新日期:2019-05-17 00:00:00

  • Characterization of the endoribonuclease active site of human apurinic/apyrimidinic endonuclease 1.

    abstract::Apurinic/apyrimidinic endonuclease 1 (APE1) is the major mammalian enzyme in DNA base excision repair that cleaves the DNA phosphodiester backbone immediately 5' to abasic sites. Recently, we identified APE1 as an endoribonuclease that cleaves a specific coding region of c-myc mRNA in vitro, regulating c-myc mRNA leve...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.06.050

    authors: Kim WC,Berquist BR,Chohan M,Uy C,Wilson DM 3rd,Lee CH

    更新日期:2011-09-02 00:00:00

  • Three-state model for lysozyme folding: triangular folding mechanism with an energetically trapped intermediate.

    abstract::We investigated the role of a partially folded intermediate that transiently accumulates during lysozyme folding. Previous studies had shown that the partially folded intermediate is located on a slow-folding pathway and that an additional fast direct pathway from the unfolded state to the native state exists. Kinetic...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1030

    authors: Wildegger G,Kiefhaber T

    更新日期:1997-07-11 00:00:00

  • Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin.

    abstract::To study mechanisms of nucleosome positioning, small circular plasmids were constructed, assembled into chromatin in vivo in Saccharomyces cerevisiae, and their chromatin structures were analysed with respect to positions of nucleosomes and nuclease-sensitive regions. Plasmids used include insertions of the URA3 gene ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90291-3

    authors: Thoma F

    更新日期:1986-07-20 00:00:00

  • The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site.

    abstract::The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.12.007

    authors: Baird-Titus JM,Clark-Baldwin K,Dave V,Caperelli CA,Ma J,Rance M

    更新日期:2006-03-10 00:00:00

  • The serine protease inhibitor canonical loop conformation: examples found in extracellular hydrolases, toxins, cytokines and viral proteins.

    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

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3389

    authors: Jackson RM,Russell RB

    更新日期:2000-02-18 00:00:00

  • Searching for potential Z-DNA in genomic Escherichia coli DNA.

    abstract::The Clarke-Carbon library with Escherichia coli DNA cloned into plasmid ColE1 was partially screened for Z-DNA with the monoclonal antibody Z-D11 using the retardation of the covalently closed circular DNA-protein complex by nitrocellulose filters. About 85% of the plasmids tested at "natural" supercoil density bound ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90259-2

    authors: Hoheisel JD,Pohl FM

    更新日期:1987-02-05 00:00:00

  • Distribution of surface-exposed and non-accessible amino acid sequences among the two major structural domains of the S-layer protein of Aeromonas salmonicida.

    abstract::The tetragonally arranged crystalline surface protein array (A-layer) of the fish pathogenic bacterium Aeromonas salmonicida is a virulence factor. Circular dichroism studies in the presence or absence of 0.1% sodium dodecyl sulfate showed that the secondary structure of A-protein, and its 39,439 molecular weight amin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1550

    authors: Doig P,McCubbin WD,Kay CM,Trust TJ

    更新日期:1993-10-20 00:00:00

  • What makes Ras an efficient molecular switch: a computational, biophysical, and structural study of Ras-GDP interactions with mutants of Raf.

    abstract::Ras is a small GTP-binding protein that is an essential molecular switch for a wide variety of signaling pathways including the control of cell proliferation, cell cycle progression and apoptosis. In the GTP-bound state, Ras can interact with its effectors, triggering various signaling cascades in the cell. In the GDP...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.03.046

    authors: Filchtinski D,Sharabi O,Rüppel A,Vetter IR,Herrmann C,Shifman JM

    更新日期:2010-06-11 00:00:00

  • Enhancing the contrast of ApoB to locate the surface components in the 3D density map of human LDL.

    abstract::A 26 Å resolution map of the structure of human low-density lipoprotein (LDL) was obtained from electron cryomicroscopy and single-particle image reconstruction. The structure showed a discoidal-shaped LDL particle with high-density regions mainly distributed at the edge of the particle and low-density regions at the ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.10.034

    authors: Liu Y,Atkinson D

    更新日期:2011-01-07 00:00:00

  • Modifying Chromatin by Histone Tail Clipping.

    abstract::Post-translational modifications (PTMs) of histone proteins play a crucial role in the regulation of chromatin structure and functions. Studies in the last few decades have revealed the significance of histone PTMs in key cellular processes including DNA replication, repair, transcription, apoptosis and cell cycle reg...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2018.07.013

    authors: Azad GK,Swagatika S,Kumawat M,Kumawat R,Tomar RS

    更新日期:2018-09-14 00:00:00

  • Functional interplay between CBP and PCAF in acetylation and regulation of transcription factor KLF13 activity.

    abstract::The transcriptional co-activators CBP/p300 and PCAF participate in transcriptional activation by many factors. We have shown that both CBP/p300 and PCAF stimulate the transcriptional activation by KLF13, a member of the KLF/Sp1 family, either individually or cooperatively. Here we further investigated how CBP and PCAF...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00429-7

    authors: Song CZ,Keller K,Chen Y,Stamatoyannopoulos G

    更新日期:2003-05-30 00:00:00

  • Complementary DNA sequence of a human cytoplasmic actin. Interspecies divergence of 3' non-coding regions.

    abstract::We have isolated and sequenced a cloned complementary DNA insert complementary to the messenger RNA of a cytoplasmic actin expressed in human epidermal cells. This provides the first cytoplasmic actin complementary DNA sequence for a vertebrate organism. The actin amino acid sequence predicted from this complementary ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(83)90117-1

    authors: Hanukoglu I,Tanese N,Fuchs E

    更新日期:1983-02-05 00:00:00

  • Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA.

    abstract::Methyltransferases from the m(1)A(58) tRNA methyltransferase (TrmI) family catalyze the S-adenosyl-l-methionine-dependent N(1)-methylation of tRNA adenosine 58. The crystal structure of Thermus thermophilus TrmI, in complex with S-adenosyl-l-homocysteine, was determined at 1.7 A resolution. This structure is closely r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.01.041

    authors: Barraud P,Golinelli-Pimpaneau B,Atmanene C,Sanglier S,Van Dorsselaer A,Droogmans L,Dardel F,Tisné C

    更新日期:2008-03-21 00:00:00

  • Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2.

    abstract::The excessive activity of matrix metalloproteinases (MMPs) contributes to pathological processes such as arthritis, tumor growth and metastasis if not balanced by the tissue inhibitors of metalloproteinases (TIMPs). In arthritis, the destruction of fibrillar (type II) collagen is one of the hallmarks, with MMP-1 (coll...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.072

    authors: Maskos K,Lang R,Tschesche H,Bode W

    更新日期:2007-03-02 00:00:00

  • Crystallization and preliminary X-ray analysis of gamma-glutamyltranspeptidase from Escherichia coli K-12.

    abstract::gamma-Glutamyltranspeptidase (EC 2.3.2.2) from Escherichia coli K-12 has been purified and crystallized by means of vapor diffusion in hanging drops. Two kinds of crystals on cell dimensions were found for X-ray diffraction analysis, one from ammonium sulfate and the other from polyethylene glycol 6000 as precipitants...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1677

    authors: Kumagai H,Nohara S,Suzuki H,Hashimoto W,Yamamoto K,Sakai H,Sakabe K,Fukuyama K,Sakabe N

    更新日期:1993-12-20 00:00:00

  • Molecular insights into the interaction between alpha-synuclein and docosahexaenoic acid.

    abstract::alpha-Synuclein (alpha-syn) is a 140-residue protein of unknown function, involved in several neurodegenerative disorders, such as Parkinson's disease. Recently, the possible interaction between alpha-syn and polyunsaturated fatty acids has attracted a strong interest. Indeed, lipids are able to trigger the multimeriz...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.09.008

    authors: De Franceschi G,Frare E,Bubacco L,Mammi S,Fontana A,de Laureto PP

    更新日期:2009-11-20 00:00:00

  • In-vivo degradation pathway of an excised intervening sequence.

    abstract::A study of the distribution in heterogeneous nuclear RNP (hnRNP) of the different forms of the first intervening sequence (IVSI) from the E3 transcription unit of adenovirus serotype 2 suggests a three-step pathway for IVS excision and degradation. First, the lariat IVS is formed in a large RNP of the size of premesse...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90480-3

    authors: Sittler A,Gallinaro H,Kister L,Jacob M

    更新日期:1987-10-20 00:00:00

  • The type I restriction endonuclease R.EcoR124I: over-production and biochemical properties.

    abstract::In this paper we describe a two-plasmid system which allows over-production of the R.EcoR124I restriction endonuclease. The endonuclease has been purified to homogeneity in milligram amounts and has been shown to be fully active for both restriction and modification. Unexpectedly, the enzyme was found to require only ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0217

    authors: Janscak P,Abadjieva A,Firman K

    更新日期:1996-04-19 00:00:00