当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Crystallization of transmembrane proteins in cubo: mechanisms of crystal growth and defect formation.

Crystallization of transmembrane proteins in cubo: mechanisms of crystal growth and defect formation.

Abstract：

:Crystallization of membrane proteins is a major stumbling block en route to elucidating their structure and understanding their function. The novel concept of membrane protein crystallization from lipidic cubic phases, "in cubo", has yielded well-ordered crystals and high-resolution structures of several membrane proteins, yet progress has been slow due to the lack of understanding of the molecular mechanisms of protein transport, crystal nucleation, growth, and defect formation in cubo. Here, we examine at molecular and mesoscopic resolution with atomic force microscopy the morphology of in cubo grown bacteriorhodopsin crystals in inert buffers and during etching by detergent. The results reveal that crystal nucleation occurs following local rearrangement of the highly curved lipidic cubic phase into a lamellar structure, which is akin to that of the native membrane. Crystals grow within the bulk cubic phase surrounded by such lamellar structures, whereby transport towards a growing crystalline layer is constrained to within an individual lamella. This mechanism leads to lack of dislocations, generation of new crystalline layers at numerous locations, and to voids and block boundaries. The characteristic macroscopic lengthscale of these defects suggests that the crystals grow by attachment of single molecules to the nuclei. These insights into the mechanisms of nucleation, growth and transport in cubo provide guidance en route to a rational design of membrane protein crystallization, and promise to further advance the field.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Qutub Y,Reviakine I,Maxwell C,Navarro J,Landau EM,Vekilov PG

doi

10.1016/j.jmb.2004.09.022

keywords:

subject

Has Abstract

pub_date

2004-11-05 00:00:00

pages

1243-54

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(04)01164-7

journal_volume

343

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Organization of the R family and other interspersed repetitive DNA sequences in the mouse genome.

    abstract：:Six R sequences have been described as members of a new family of dispersed repetitive DNA in the mouse genome (Gebhard et al., 1982). Several sequenced regions were extended in the 5' direction (R1, R2 and R6) and two new sequences were determined (R7 and R8). On the basis of our sequence and blot hybridization data ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(83)80147-8

    authors： Gebhard W,Zachau HG

    更新日期：1983-10-25 00:00:00

  • Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface.

    abstract：:MEF2 and NKX2-5 transcription factors interact with each other in cardiogenesis and are necessary for normal heart formation. Despite evidence suggesting that these two transcription factors function synergistically and possibly through direct physical interactions, molecular mechanisms by which they interact are not ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.07.004

    authors： Lei X,Zhao J,Sagendorf JM,Rajashekar N,Xu J,Dantas Machado AC,Sen C,Rohs R,Feng P,Chen L

    更新日期：2020-09-04 00:00:00

  • Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding.

    abstract：:We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume approximately 150 A(3) that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystal...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.10.086

    authors： Liu L,Baase WA,Matthews BW

    更新日期：2009-01-16 00:00:00

  • Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures.

    abstract：:We carry out a theoretical study of the vibrational and relaxation properties of naturally occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model, we provide a full characterization of the spectrum and eigenmodes of vibration at various tempe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00710-6

    authors： Micheletti C,Lattanzi G,Maritan A

    更新日期：2002-08-30 00:00:00

  • Splicing of a cap-proximal human Papillomavirus 16 E6E7 intron promotes E7 expression, but can be restrained by distance of the intron from its RNA 5' cap.

    abstract：:Human papillomavirus 16 (HPV16) E6E7 pre-mRNA is bicistronic and has an intron in the E6 coding region with one 5' splice site and two alternative 3' splice sites, which produce E6(*)I and E6(*)II, respectively. If this intron remains unspliced, the resulting E6E7 mRNA expresses oncogenic E6. We found for the first ti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.02.023

    authors： Zheng ZM,Tao M,Yamanegi K,Bodaghi S,Xiao W

    更新日期：2004-04-09 00:00:00

  • Genetic selection for critical residues in ribonucleases.

    abstract：:Homologous mammalian proteins were subjected to an exhaustive search for residues that are critical to their structure/function. Error-prone polymerase chain reactions were used to generate random mutations in the genes of bovine pancreatic ribonuclease (RNase A) and human angiogenin, and a genetic selection based on ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.07.020

    authors： Smith BD,Raines RT

    更新日期：2006-09-22 00:00:00

  • Turn nucleation perturbs amyloid β self-assembly and cytotoxicity.

    abstract：:The accumulation of senile plaques composed of amyloid β (Aβ) fibrils is a hallmark of Alzheimer's disease, although prefibrillar oligomeric species are believed to be the primary neurotoxic congeners in the pathogenesis of Alzheimer's disease. Uncertainty regarding the mechanistic relationship between Aβ oligomer and...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.01.055

    authors： Doran TM,Anderson EA,Latchney SE,Opanashuk LA,Nilsson BL

    更新日期：2012-08-10 00:00:00

  • Structure of the Top a-t component of alfalfa mosaic virus. A non-icosahedral virion.

    abstract：:Neutron-scattering in combination with quasi-elastic light-scattering and electron microscopy was used to derive a model for the capsid structure of the Top a-t component of alfalfa mosaic virus (AMV-Ta-t). In the electron microscope, AMV-Ta-t appears as an irregular ellipsoidal particle with apparent dimensions 275 (...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(83)80350-7

    authors： Cusack S,Oostergetel GT,Krijgsman PC,Mellema JE

    更新日期：1983-12-05 00:00:00

  • Sequence-specific DNA binding of the phage Mu C protein: footprinting analysis reveals altered DNA conformation upon protein binding.

    abstract：:The mom gene of bacteriophage Mu, which codes for a DNA modification function, is regulated in a complex manner at both transcriptional and translational levels. The phage-encoded C protein functions as an activator of mom transcription. The mom promoter has features of an activator-dependent weak promoter, and the C ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0379

    authors： Ramesh V,Nagaraja V

    更新日期：1996-07-05 00:00:00

  • Conformation of BCL-XL upon Membrane Integration.

    abstract：:BCL-XL is an anti-apoptotic BCL-2 family protein found both in the cytosol and bound to intracellular membranes. Structural studies of BCL-XL have advanced by deleting its hydrophobic C-terminus and adding detergents to enhance solubility. However, since the C-terminus is essential for function and detergents strongly...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.02.019

    authors： Yao Y,Fujimoto LM,Hirshman N,Bobkov AA,Antignani A,Youle RJ,Marassi FM

    更新日期：2015-07-03 00:00:00

  • Generation of mutated variants of the human form of the MHC class I-related receptor, FcRn, with increased affinity for mouse immunoglobulin G.

    abstract：:Much data support the concept that the MHC class I-related receptor FcRn serves to regulate immunoglobulin G (IgG) concentrations in serum and other diverse body sites in both rodents and humans. Previous studies have indicated that the human ortholog of FcRn is endowed with unexpectedly high stringency in binding spe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00952-5

    authors： Zhou J,Johnson JE,Ghetie V,Ober RJ,Ward ES

    更新日期：2003-09-26 00:00:00

  • Reverse turns in blocked dipeptides are intrinsically unstable in water.

    abstract：:We have carried out molecular dynamics simulations to study the conformational equilibria of two blocked dipeptides, Ac-Ala-Ala-NHMe and trans-Ac-Pro-Ala-NHMe, in water (Ac, amino-terminal blocking group COCH3; NHMe, carboxy-terminal blocking group NHCH3). Using specialized sampling techniques we computed free-energy ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90399-7

    authors： Tobias DJ,Sneddon SF,Brooks CL 3rd

    更新日期：1990-12-05 00:00:00

  • Positioning membrane proteins by novel protein engineering and biophysical approaches.

    abstract：:Membrane proteins are unique, in that they can function properly only when they are bound to cellular membranes in a distinct manner. Therefore, positioning of membrane proteins with respect to the membrane is required in addition to the three-dimensional structures in order to understand their detailed molecular mech...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.06.080

    authors： Tatulian SA,Qin S,Pande AH,He X

    更新日期：2005-09-02 00:00:00

  • Recognition of the highly conserved GTPase center of 23 S ribosomal RNA by ribosomal protein L11 and the antibiotic thiostrepton.

    abstract：:The antibiotic thiostrepton, a thiazole-containing peptide, inhibits translation and ribosomal GTPase activity by binding directly to a limited and highly conserved region of the large subunit ribosomal RNA termed the GTPase center. We have previously used a filter binding assay to examine the binding of ribosomal pro...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90932-v

    authors： Ryan PC,Lu M,Draper DE

    更新日期：1991-10-20 00:00:00

  • A novel allosteric mechanism in haemoglobin. Structure of bovine deoxyhaemoglobin, absence of specific chloride-binding sites and origin of the chloride-linked Bohr effect in bovine and human haemoglobin.

    abstract：:The structure of bovine deoxyhaemoglobin has been determined at 2.2 A resolution and refined to an R-factor of 0.193 for all 32,583 reflections, and a free R-factor of 0.249 for 1527 reflections excluded from the refinement. The structure shows no significant differences between the alpha-carbon positions of bovine an...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1530

    authors： Perutz MF,Fermi G,Poyart C,Pagnier J,Kister J

    更新日期：1993-10-05 00:00:00

  • The alternatively folded state of the antibody C(H)3 domain.

    abstract：:The C(H)3 domain of antibodies is characterized by two antiparallel beta-sheets forming a disulfide-linked sandwich-like structure. At acidic pH values and low ionic strength, C(H)3 becomes completely unfolded. The addition of salt transforms the acid-unfolded protein into an alternatively folded state exhibiting a ch...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4707

    authors： Thies MJ,Kammermeier R,Richter K,Buchner J

    更新日期：2001-06-22 00:00:00

  • Refined structure of the nicotinic acetylcholine receptor at 4A resolution.

    abstract：:We present a refined model of the membrane-associated Torpedo acetylcholine (ACh) receptor at 4A resolution. An improved experimental density map was obtained from 342 electron images of helical tubes, and the refined structure was derived to an R-factor of 36.7% (R(free) 37.9%) by standard crystallographic methods, a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.12.031

    authors： Unwin N

    更新日期：2005-03-04 00:00:00

  • A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch.

    abstract：:Riboswitches are noncoding RNA elements that are commonly found in the 5'-untranslated region of bacterial mRNA. Binding of a small-molecule metabolite to the riboswitch aptamer domain guides the folding of the downstream sequence into one of two mutually exclusive secondary structures that directs gene expression. Th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.10.074

    authors： Edwards AL,Batey RT

    更新日期：2009-01-23 00:00:00

  • Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.

    abstract：:Selenophosphate synthetase (SPS) catalyzes the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential reactive selenium donor for the formation of selenocysteine (Sec) and 2-selenouridine residues in proteins and RNAs, respectively. Many SPS are themselves Sec-containing...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.08.042

    authors： Itoh Y,Sekine S,Matsumoto E,Akasaka R,Takemoto C,Shirouzu M,Yokoyama S

    更新日期：2009-02-06 00:00:00

  • Antibody-antigen interactions: contact analysis and binding site topography.

    abstract：:We have analysed antigen-contacting residues and combining site shape in the antibody Fv and Fab crystal structures now available from the Protein Data Bank. Antigen-contacting propensities are presented for each antibody residue, allowing a new definition for the complementarity determining regions (CDRs) to be propo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0548

    authors： MacCallum RM,Martin AC,Thornton JM

    更新日期：1996-10-11 00:00:00

  • Functional characterization and modulation of the DNA cleavage efficiency of type III restriction endonuclease EcoP15I in its interaction with two sites in the DNA target.

    abstract：:EcoP15I is a Type III restriction endonuclease requiring the interaction with two inversely oriented 5'-CAGCAG recognition sites for efficient DNA cleavage. Diverse models have been developed to explain how enzyme complexes bound to both sites move toward each other, DNA translocation, DNA looping and simple diffusion...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.02.047

    authors： Möncke-Buchner E,Rothenberg M,Reich S,Wagenführ K,Matsumura H,Terauchi R,Krüger DH,Reuter M

    更新日期：2009-04-17 00:00:00

  • Crystal structure of the Vibrio cholerae cytolysin (VCC) pro-toxin and its assembly into a heptameric transmembrane pore.

    abstract：:Pathogenic Vibrio cholerae secrete V. cholerae cytolysin (VCC), an 80 kDa pro-toxin that assembles into an oligomeric pore on target cell membranes following proteolytic cleavage and interaction with cell surface receptors. To gain insight into the activation and targeting activities of VCC, we solved the crystal stru...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.05.045

    authors： Olson R,Gouaux E

    更新日期：2005-07-29 00:00:00

  • Inter-domain motions of the N-domain of the KdpFABC complex, a P-type ATPase, are not driven by ATP-induced conformational changes.

    abstract：:P-type ATPases are involved in the active transport of ions across biological membranes. The KdpFABC complex (P-type ATPase) of Escherichia coli is a high-affinity K+ uptake system that operates only when the cell experiences osmotic stress or K+ limitation. Here, we present the solution structure of the nucleotide bi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.07.060

    authors： Haupt M,Bramkamp M,Coles M,Altendorf K,Kessler H

    更新日期：2004-10-01 00:00:00

  • Fourteen protomers compose the oligomer III of the proton-rotor in spinach chloroplast ATP synthase.

    abstract：:Three fundamentally different chloroplast ATP synthase samples of increasing complexity were visualized by atomic force microscopy. The samples are distinguishable in respect to the isolation technique, the detergent employed, and the final subunit composition. The homo-oligomer III was isolated following SDS treatmen...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.08.046

    authors： Seelert H,Dencher NA,Müller DJ

    更新日期：2003-10-17 00:00:00

  • Characterization of in vitro and in vivo mutations in non-conserved nucleotides in the ribosomal RNA recognition domain for the ribotoxins ricin and sarcin and the translation elongation factors.

    abstract：:The sarcin/ricin domain in 23 S/28 S rRNA is crucial for ribosome function, since it constitutes at least part of the binding site for the elongation factors and hence is essential for binding aminoacyl-tRNA and for translocation. The domain is also the site of action of ricin and sarcin and analysis of the effect of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2337

    authors： Macbeth MR,Wool IG

    更新日期：1999-01-15 00:00:00

  • Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein.

    abstract：:Proteins with ultra-fast folding/unfolding kinetics are excellent candidates for study by molecular dynamics. Here, we describe such simulations of a three helix bundle protein, the engrailed homeodomain (En-HD), which folds via the diffusion-collision model. The unfolding pathway of En-HD was characterized by seven s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.06.074

    authors： DeMarco ML,Alonso DO,Daggett V

    更新日期：2004-08-20 00:00:00

  • Mutational analysis of the conserved bases C1402 and A1500 in the center of the decoding domain of Escherichia coli 16 S rRNA reveals an important tertiary interaction.

    abstract：:Interactions within the decoding center of the 30 S ribosomal subunit have been investigated by constructing all 15 possible mutations at nucleotides C1402 and A1500 in helix 44 of 16 S rRNA. As expected, most of the mutations resulted in highly deleterious phenotypes, consistent with the high degree of conservation o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4576

    authors： Vila-Sanjurjo A,Dahlberg AE

    更新日期：2001-05-04 00:00:00

  • Congenital Cataract-Causing Mutation G129C in γC-Crystallin Promotes the Accumulation of Two Distinct Unfolding Intermediates That Form Highly Toxic Aggregates.

    abstract：:Cataract is a lens opacification disease prevalent worldwide. Cataract-causing mutations in crystallins generally lead to the formation of light-scattering particles in the lens. However, it remains unclear for the detailed structural and pathological mechanisms of most mutations. In this study, we showed that the G12...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.07.001

    authors： Xi YB,Chen XJ,Zhao WJ,Yan YB

    更新日期：2015-08-28 00:00:00

  • Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures.

    abstract：:Atomic positions obtained by X-ray crystallography are time and space averages over many molecules in the crystal. Importantly, interatomic distances, calculated between such average positions and frequently used in structural and mechanistic analyses, can be substantially different from the more appropriate time-aver...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.05.033

    authors： Kuzmanic A,Kruschel D,van Gunsteren WF,Pannu NS,Zagrovic B

    更新日期：2011-08-05 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