Articles

Annual acknowledgement of manuscript reviewers

The editors of BMC Structural Biology would like to thank all of our reviewers who have contributed to the journal in Volume 13 (2013).

Authors: Simon Harold

PcrG protects the two long helical oligomerization domains of PcrV, by an interaction mediated by the intramolecular coiled-coil region of PcrG

PcrV is a hydrophilic translocator of type three secretion system (TTSS) and a structural component of the functional translocon. C-terminal helix of PcrV is essential for its oligomerization at the needle tip...

Authors: Abhishek Basu, Urmisha Das, Supratim Dey and Saumen Datta

Synthetic cationic antimicrobial peptides bind with their hydrophobic parts to drug site II of human serum albumin

Many biologically active compounds bind to plasma transport proteins, and this binding can be either advantageous or disadvantageous from a drug design perspective. Human serum albumin (HSA) is one of the most...

Authors: Annfrid Sivertsen, Johan Isaksson, Hanna-Kirsti S Leiros, Johan Svenson, John-Sigurd Svendsen and Bjørn Olav Brandsdal

Crystal structures of the human Dysferlin inner DysF domain

Mutations in dysferlin, the first protein linked with the cell membrane repair mechanism, causes a group of muscular dystrophies called dysferlinopathies. Dysferlin is a type two-anchored membrane protein, wit...

Authors: Altin Sula, Ambrose R Cole, Corin Yeats, Christine Orengo and Nicholas H Keep

Dimeric structure of p300/CBP associated factor

p300/CBP associating factor (PCAF, also known as KAT2B for lysine acetyltransferase 2B) is a catalytic subunit of megadalton metazoan complex ATAC (Ada-Two-A containing complex) for acetylation of histones. Ho...

Authors: Shasha Shi, Juanyu Lin, Yongfei Cai, Jiao Yu, Haiyan Hong, Kunmei Ji, Jennifer S Downey, Xiaodong Lu, Ruichuan Chen, Jiahuai Han and Aidong Han

Crystal structures of IspF from Plasmodium falciparum and Burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment

2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) catalyzes the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate and cytidine monophosph...

Authors: Patrick EF O’Rourke, Justyna Kalinowska-Tłuścik, Paul K Fyfe, Alice Dawson and William N Hunter

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools i...

Authors: Manuel Rueda, Modesto Orozco, Maxim Totrov and Ruben Abagyan

Structure of the S100A4/myosin-IIA complex

S100A4, a member of the S100 family of Ca²⁺-binding proteins, modulates the motility of both non-transformed and cancer cells by regulating the localization and stability of cellular protrusions. Biochemical stud...

Authors: Udupi A Ramagopal, Natalya G Dulyaninova, Kristen M Varney, Paul T Wilder, Sridevi Nallamsetty, Michael Brenowitz, David J Weber, Steven C Almo and Anne R Bresnick

Crystal structure of the γ-hydroxymuconic semialdehyde dehydrogenase from Pseudomonas sp. strainWBC-3, a key enzyme involved in para-Nitrophenol degradation

para-Nitrophenol (PNP) is a highly toxic compound with threats to mammalian health. The pnpE-encoded γ-hydroxymuconic semialdehyde dehydrogenase catalyzes the reduction of γ-hydroxymuconic semialdehyde to maleyl...

Authors: Jing Su, Cong Zhang, Jun-Jie Zhang, Tiandi Wei, Deyu Zhu, Ning-Yi Zhou and Li chuan Gu

Effect of intracellular loop 3 on intrinsic dynamics of human β₂-adrenergic receptor

To understand the effect of the long intracellular loop 3 (ICL3) on the intrinsic dynamics of human β₂-adrenergic receptor, molecular dynamics (MD) simulations were performed on two different models, both of whic...

Authors: Ozer Ozcan, Arzu Uyar, Pemra Doruker and Ebru Demet Akten

The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases

Malyl-CoA lyase (MCL) is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related Coenzyme A (CoA) thioesters. This enzyme plays a crucial, multifunctional role in ...

Authors: Jan Zarzycki and Cheryl A Kerfeld

DINC: A new AutoDock-based protocol for docking large ligands

Using the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standar...

Authors: Ankur Dhanik, John S McMurray and Lydia E Kavraki

An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility

Conformational flexibility creates errors in the comparison of protein structures. Even small changes in backbone or sidechain conformation can radically alter the shape of ligand binding cavities. These chang...

Authors: Brian G Godshall, Yisheng Tang, Wenjie Yang and Brian Y Chen

Unbiased, scalable sampling of protein loop conformations from probabilistic priors

Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search...

Authors: Yajia Zhang and Kris Hauser

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajector...

Authors: Kevin Molloy and Amarda Shehu

A conservation and biophysics guided stochastic approach to refining docked multimeric proteins

We introduce a protein docking refinement method that accepts complexes consisting of any number of monomeric units. The method uses a scoring function based on a tight coupling between evolutionary conservati...

Authors: Bahar Akbal-Delibas and Nurit Haspel

A conservation and rigidity based method for detecting critical protein residues

Certain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved res...

Authors: Bahar Akbal-Delibas, Filip Jagodzinski and Nurit Haspel

Estimating loop length from CryoEM images at medium resolutions

De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the lo...

Authors: Andrew McKnight, Dong Si, Kamal Al Nasr, Andrey Chernikov, Nikos Chrisochoides and Jing He

A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction

Elucidating the native structure of a protein molecule from its sequence of amino acids, a problem known as de novo structure prediction, is a long standing challenge in computational structural biology. Diffi...

Authors: Sameh Saleh, Brian Olson and Amarda Shehu

Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce

Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Their secondary structures are crucial for the RNA functionality, and the prediction...

Authors: Boyu Zhang, Daniel T Yehdego, Kyle L Johnson, Ming-Ying Leung and Michela Taufer

Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods

Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important...

Authors: Ibrahim Al-Bluwi, Marc Vaisset, Thierry Siméon and Juan Cortés

Four-body atomic potential for modeling protein-ligand binding affinity: application to enzyme-inhibitor binding energy prediction

Models that are capable of reliably predicting binding affinities for protein-ligand complexes play an important role the field of structure-guided drug design.

Authors: Majid Masso

The 6th Computational Structural Bioinformatics Workshop

Authors: Jing He, Amarda Shehu, Nurit Haspel and Brian Chen

Structural insights into Resveratrol’s antagonist and partial agonist actions on estrogen receptor alpha

Resveratrol, a naturally occurring stilbene, has been categorized as a phytoestrogen due to its ability to compete with natural estrogens for binding to estrogen receptor alpha (ERα) and modulate the biologica...

Authors: Sandipan Chakraborty, Anait S Levenson and Pradip K Biswas

Type I pyridoxal 5′-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines

Pyridoxal 5′-phosphate (PLP)-dependent enzymes of fold type I, the most studied structural class of the PLP-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. These en...

Authors: Teresa Milano, Alessandro Paiardini, Ingeborg Grgurina and Stefano Pascarella

gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy

Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often ...

Authors: Thai V Hoang, Xavier Cavin, Patrick Schultz and David W Ritchie

Quantification of the impact of PSI:Biology according to the annotations of the determined structures

Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third p...

Authors: Paul J DePietro, Elchin S Julfayev and William A McLaughlin

Structural and biochemical characterization of the essential DsbA-like disulfide bond forming protein from Mycobacterium tuberculosis

Bacterial D is ulfide b ond forming (Dsb) proteins facilitate proper folding and disulfide bond formation of periplasmic and secreted proteins. Previously, we have shown that Mycobacterium tuberculosis Mt-DsbE an...

Authors: Nicholas Chim, Christine A Harmston, David J Guzman and Celia W Goulding

Structural and functional characterisation of the methionine adenosyltransferase from Thermococcus kodakarensis

Methionine adenosyltransferases catalyse the synthesis of S-adenosylmethionine, a cofactor abundant in all domains of life. In contrast to the enzymes from bacteria and eukarya that show high sequence similarity,...

Authors: Julia Schlesier, Jutta Siegrist, Stefan Gerhardt, Annette Erb, Simone Blaesi, Michael Richter, Oliver Einsle and Jennifer N Andexer

An analysis of oligomerization interfaces in transmembrane proteins

The amount of transmembrane protein (TM) structures solved to date is now large enough to attempt large scale analyses. In particular, extensive studies of oligomeric interfaces in the transmembrane region are...

Authors: Jose M Duarte, Nikhil Biyani, Kumaran Baskaran and Guido Capitani

Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture

Assessing protein modularity is important to understand protein evolution. Still the question of the existence of a sub-domain modular architecture remains. We propose a graph-theory approach with significance...

Authors: Jose Sergio Hleap, Edward Susko and Christian Blouin

Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold

Increasing rates of antimicrobial resistance among uropathogens led, among other efforts, to the application of subtractive reverse vaccinology for the identification of antigens present in extraintestinal pat...

Authors: Dunja Urosev, Mario Ferrer-Navarro, Ilaria Pastorello, Elena Cartocci, Lionel Costenaro, Dmitrijs Zhulenkovs, Jean-Didier Maréchal, Ainars Leonchiks, David Reverter, Laura Serino, Marco Soriani and Xavier Daura

Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein

Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of...

Authors: Parthapratim Munshi, Christopher B Stanley, Sudipa Ghimire-Rijal, Xun Lu, Dean A Myles and Matthew J Cuneo

Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a β-solenoid structure

The human mineralocorticoid receptor (MR) is one of the main components of the renin-angiotensin-aldosterone system (RAAS), the system that regulates the body exchange of water and sodium. The evolutionary ori...

Authors: Metaxia Vlassi, Katharina Brauns and Miguel A Andrade-Navarro

Detection of persistent organic pollutants binding modes with androgen receptor ligand binding domain by docking and molecular dynamics

Persistent organic pollutants (POPs) are persistent in the environment after release from industrial compounds, combustion productions or pesticides. The exposure of POPs has been related to various reproducti...

Authors: Xian Jin Xu, Ji Guo Su, Anna Rita Bizzarri, Salvatore Cannistraro, Ming Liu, Yi Zeng, Wei Zu Chen and Cun Xin Wang

Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure

The arginine of the D/E/NRY motif in Rhodopsin family G protein-coupled receptors (GPCRs) is conserved in 96% of these proteins. In some GPCRs, this arginine in transmembrane 3 can form a salt bridge with an a...

Authors: Margaret M Pruitt, Monica H Lamm and Clark R Coffman

Crosslinking and mass spectrometry suggest that the isolated NTD domain dimer of Moloney murine leukemia virus integrase adopts a parallel arrangement in solution

Retroviral integrases (INs) catalyze the integration of viral DNA in the chromosomal DNA of the infected cell. This reaction requires the multimerization of IN to coordinate a nucleophilic attack of the 3’ end...

Authors: Daniel R Henriquez, Caifeng Zhao, Haiyan Zheng, José J Arbildua, Mónica L Acevedo, Monica J Roth and Oscar Leon

Crystal structure of signal regulatory protein gamma (SIRPγ) in complex with an antibody Fab fragment

Signal Regulatory Protein γ (SIRPγ) is a member of a closely related family of three cell surface receptors implicated in modulating immune/inflammatory responses. SIRPγ is expressed on T lymphocytes where it ...

Authors: Joanne E Nettleship, Jingshan Ren, David J Scott, Nahid Rahman, Deborah Hatherley, Yuguang Zhao, David I Stuart, A Neil Barclay and Raymond J Owens

The UmuC subunit of the E. coli DNA polymerase V shows a unique interaction with the β-clamp processivity factor

Strict regulation of replisome components is essential to ensure the accurate transmission of the genome to the next generation. The sliding clamp processivity factors play a central role in this regulation, i...

Authors: Atif A Patoli, Jody A Winter and Karen A Bunting

Crystal structure of the C-terminal globular domain of the third paralog of the Archaeoglobus fulgidus oligosaccharyltransferases

Protein N-glycosylation occurs in the three domains of life. Oligosaccharyltransferase (OST) transfers an oligosaccharide chain to the asparagine residue in the N-glycosylation sequons. The catalytic subunits ...

Authors: Shunsuke Matsumoto, Atsushi Shimada and Daisuke Kohda

Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B₁₂) biosynthesis

In the anaerobic pathway of cobalamin (vitamin B₁₂) synthesis, the CbiT enzyme plays two roles, as a cobalt-precorrin-7 C15-methyltransferase and a C12-decarboxylase, to produce the intermediate, cobalt-precorrin...

Authors: Balasundaram Padmanabhan, Shigeyuki Yokoyama and Yoshitaka Bessho

Helical ambivalency induced by point mutations

Mutation of amino acid sequences in a protein may have diverse effects on its structure and function. Point mutations of even a single amino acid residue in the helices of the non-redundant database may lead t...

Authors: Nicholus Bhattacharjee and Parbati Biswas

A structural role for the PHP domain in E. coli DNA polymerase III

In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of som...

Authors: Tiago Barros, Joel Guenther, Brian Kelch, Jordan Anaya, Arjun Prabhakar, Mike O’Donnell, John Kuriyan and Meindert H Lamers

Localization of putative binding sites for cyclic guanosine monophosphate and the anti-cancer drug 5-fluoro-2′-deoxyuridine-5′-monophosphate on ABCC11 in silico models

The Multidrug Resistance Protein ABCC11/MRP8 is expressed in physiological barriers and tumor breast tissues in which it secretes various substrates including cGMP (cyclic guanosine monophosphate) and 5FdUMP (...

Authors: Mylène Honorat, Raphaël Terreux, Pierre Falson, Attilio Di Pietro, Charles Dumontet and Lea Payen

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach

The post-genomic era poses several challenges. The biggest is the identification of biochemical function for protein sequences and structures resulting from genomic initiatives. Most sequences lack a character...

Authors: Rajaram Gana, Shruti Rao, Hongzhan Huang, Cathy Wu and Sona Vasudevan

Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC

Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specifi...

Authors: Jungwook Kim and Steven C Almo

Disturbance of DNA conformation by the binding of testosterone-based platinum drugs via groove-face and intercalative interactions: a molecular dynamics simulation study

To explore novel platinum-based anticancer agents that are distinct from the structure and interaction mode of the traditional cisplatin by forming the bifunctional intrastrand 1,2 GpG adduct, the monofunction...

Authors: Shanshan Cui, Yan Wang and Guangju Chen

The role of Cysteine 6.47 in class A GPCRs

The CWxP motif of transmembrane helix 6 (x: any residue) is highly conserved in class A GPCRs. Within this motif, W6.48 is a big star in the theory of the global “toggle switch” because of its key role in the ...

Authors: Mireia Olivella, Gianluigi Caltabiano and Arnau Cordomí

Designing and benchmarking the MULTICOM protein structure prediction system

Predicting protein structure from sequence is one of the most significant and challenging problems in bioinformatics. Numerous bioinformatics techniques and tools have been developed to tackle almost every asp...

Authors: Jilong Li, Xin Deng, Jesse Eickholt and Jianlin Cheng

Annual acknowledgement of manuscript reviewers

The editors of BMC Structural Biology would like to thank all of our reviewers who have contributed to the journal in Volume 12 (2012).

Authors: Simon Harold