Articles

Exploring the “dark matter” of a mammalian proteome by protein structure and function modeling

A growing body of evidence shows that gene products encoded by short open reading frames play key roles in numerous cellular processes. Yet, they are generally overlooked in genome assembly, escaping annotatio...

Authors: Michal Brylinski

Comparative proteomic analysis of genetically modified maize grown under different agroecosystems conditions in Brazil

Profiling technologies allow the simultaneous measurement and comparison of thousands of cell components without prior knowledge of their identity. In the present study, we used two-dimensional gel electrophor...

Authors: Sarah Zanon Agapito-Tenfen, Miguel Pedro Guerra, Odd-Gunnar Wikmark and Rubens Onofre Nodari

Surface-exposed proteins of pathogenic mycobacteria and the role of cu-zn superoxide dismutase in macrophages and neutrophil survival

Pathogenic mycobacteria are important agents causing human disease. Mycobacterium avium subsp. hominissuis (M. avium) is a species of recalcitrant environmental pathogen. The bacterium forms robust biofilms that ...

Authors: Michael McNamara, Shin-Cheng Tzeng, Claudia Maier, Martin Wu and Luiz E Bermudez

Identifying protein complexes with fuzzy machine learning model

Many computational approaches have been developed to detect protein complexes from protein-protein interaction (PPI) networks. However, these PPI networks are always built from high-throughput experiments. The...

Authors: Bo Xu, Hongfei Lin, Kavishwar B Wagholikar, Zhihao Yang and Hongfang Liu

Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles

Protein interaction networks (PINs) are known to be useful to detect protein complexes. However, most available PINs are static, which cannot reflect the dynamic changes in real networks. At present, some rese...

Authors: Qianghua Xiao, Jianxin Wang, Xiaoqing Peng and Fang-Xiang Wu

An effective evolutionary algorithm for protein folding on 3D FCC HP model by lattice rotation and generalized move sets

Proteins are essential biological molecules which play vital roles in nearly all biological processes. It is the tertiary structure of a protein that determines its functions. Therefore the prediction of a pro...

Authors: Jyh-Jong Tsay and Shih-Chieh Su

Detecting overlapping protein complexes in PPI networks based on robustness

Recently, large data sets of protein-protein interactions (PPI) which can be modeled as PPI networks are generated through high-throughput methods. And locally dense regions in PPI networks are very likely to ...

Authors: Shuliang Wang and Fang Wu

Semi-supervised method for biomedical event extraction

Biomedical extraction based on supervised machine learning still faces the problem that a limited labeled dataset does not saturate the learning method. Many supervised learning algorithms for bio-event extrac...

Authors: Jian Wang, Qian Xu, Hongfei Lin, Zhihao Yang and Yanpeng Li

PPIRank - an advanced method for ranking protein-protein interations in TAP/MS data

Tandem affinity purification coupled with mass-spectrometry (TAP/MS) analysis is a popular method for the identification of novel endogenous protein-protein interactions (PPIs) in large-scale. Computational an...

Authors: Xiaoyun Sun, Pengyu Hong, Meghana Kulkarni, Young Kwon and Norbert Perrimon

An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles

The immune system must detect a wide variety of microbial pathogens, such as viruses, bacteria, fungi and parasitic worms, to protect the host against disease. Antigenic peptides displayed by MHC II (class II ...

Authors: Wen-Jun Shen, Shaohong Zhang and Hau-San Wong

PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data

Phosphorylation site assignment of high throughput tandem mass spectrometry (LC-MS/MS) data is one of the most common and critical aspects of phosphoproteomics. Correctly assigning phosphorylated residues help...

Authors: Fahad Saeed, Trairak Pisitkun, Jason D Hoffert, Sara Rashidian, Guanghui Wang, Marjan Gucek and Mark A Knepper

Gaussian process regression model for normalization of LC-MS data using scan-level information

Differences in sample collection, biomolecule extraction, and instrument variability introduce bias to data generated by liquid chromatography coupled with mass spectrometry (LC-MS). Normalization is used to a...

Authors: Mohammad R Nezami Ranjbar, Yi Zhao, Mahlet G Tadesse, Yue Wang and Habtom W Ressom

Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter

Many problems in protein modeling require obtaining a discrete representation of the protein conformational space as an ensemble of conformations. In ab-initio structure prediction, in particular, where the go...

Authors: Brian S Olson and Amarda Shehu

The role of electrostatic energy in prediction of obligate protein-protein interactions

Prediction and analysis of protein-protein interactions (PPI) and specifically types of PPIs is an important problem in life science research because of the fundamental roles of PPIs in many biological process...

Authors: Mina Maleki, Gokul Vasudev and Luis Rueda

Peptide identification based on fuzzy classification and clustering

The sequence database searching has been the dominant method for peptide identification, in which a large number of peptide spectra generated from LC/MS/MS experiments are searched using a search engine agains...

Authors: Xijun Liang, Zhonghang Xia, Xinnan Niu, Andrew J Link, Liping Pang, Fang-Xiang Wu and Hongwei Zhang

Fully automated protein complex prediction based on topological similarity and community structure

To understand the function of protein complexes and their association with biological processes, a lot of studies have been done towards analyzing the protein-protein interaction (PPI) networks. However, the a...

Authors: Chengwei Lei, Saleh Tamim, Alexander JR Bishop and Jianhua Ruan

Ranking and compacting binding segments of protein families using aligned pattern clusters

Discovering sequence patterns with variation can unveil functions of a protein family that are important for drug discovery. Exploring protein families using existing methods such as multiple sequence alignmen...

Authors: En-Shiun Annie Lee and Andrew KC Wong

HMPAS: Human Membrane Protein Analysis System

Membrane proteins perform essential roles in diverse cellular functions and are regarded as major pharmaceutical targets. The significance of membrane proteins has led to the developing dozens of resources rel...

Authors: Min-Sung Kim and Gwan-Su Yi

HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking

Elucidating the three-dimensional structure of a higher-order molecular assembly formed by interacting molecular units, a problem commonly known as docking, is central to unraveling the molecular basis of cell...

Authors: Irina Hashmi and Amarda Shehu

Predicting beta-turns in proteins using support vector machines with fractional polynomials

β-turns are secondary structure type that have essential role in molecular recognition, protein folding, and stability. They are found to be the most common type of non-repetitive structures since 25% of amino ....

Authors: Murtada Khalafallah Elbashir, Jianxin Wang, Fang-Xiang Wu and Lusheng Wang

Identification of b-/y-ions in MS/MS spectra using a two stage neural network

Independent of the approach used, the ability to correctly interpret tandem MS data depends on the quality of the original spectra. Even in the case of the highest quality spectra, the majority of spectral pea...

Authors: James P Cleveland and John R Rose

M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations

Protein-protein interactions (PPIs) play a key role in understanding the mechanisms of cellular processes. The availability of interactome data has catalyzed the development of computational approaches to eluc...

Authors: Young-Rae Cho, Marco Mina, Yanxin Lu, Nayoung Kwon and Pietro H Guzzi

Integrating domain similarity to improve protein complexes identification in TAP-MS data

Detecting protein complexes in protein-protein interaction (PPI) networks plays an important role in improving our understanding of the dynamic of cellular organisation. However, protein interaction data gener...

Authors: Bingjing Cai, Haiying Wang, Huiru Zheng and Hui Wang

A combined approach for genome wide protein function annotation/prediction

Today large scale genome sequencing technologies are uncovering an increasing amount of new genes and proteins, which remain uncharacterized. Experimental procedures for protein function prediction are low thr...

Authors: Alfredo Benso, Stefano Di Carlo, Hafeez ur Rehman, Gianfranco Politano, Alessandro Savino and Prashanth Suravajhala

The Aeromonas salmonicida subsp. salmonicida exoproteome: global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis

Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Despite the identification of several virulence factors the pathogenesis is still poorly...

Authors: Philippe Vanden Bergh, Manfred Heller, Sophie Braga-Lagache and Joachim Frey

Quantitative proteomics reveals regulatory differences in the chondrocyte secretome from human medial and lateral femoral condyles in osteoarthritic patients

Osteoarthritis (OA) is a destructive joint disease and there are no known biomarkers available for an early diagnosis. To identify potential disease biomarkers and gain further insight into the disease mechani...

Authors: Johan Stenberg, Ulla Rüetschi, Eva Skiöldebrand, Johan Kärrholm and Anders Lindahl

The Aeromonas salmonicida subsp. salmonicida exoproteome: determination of the complete repertoire of Type-Three Secretion System effectors and identification of other virulence factors

Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Several virulence factors have been described, but the type-three secretion system (T3SS...

Authors: Philippe Vanden Bergh, Manfred Heller, Sophie Braga-Lagache and Joachim Frey

Proteomic analysis of Fusarium oxysporum f. sp. cubense tropical race 4-inoculated response to Fusarium wilts in the banana root cells

Fusarium wilt of banana is one of the most destructive diseases in the world. This disease has caused heavy losses in major banana production areas. Except for molecular breeding methods based on plant defense...

Authors: Xingshen Li, Tingting Bai, Yunfeng Li, Xiaolei Ruan and Huaping Li

The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) eggshell

Chicken eggshell mineralization is a prominent model for biomineralization not only because of its importance for avian reproduction but also because of the commercial interest associated with eggshell quality...

Authors: Karlheinz Mann and Matthias Mann

Potential biomarkers for adult acute myeloid leukemia minimal residual disease assessment searched by serum peptidome profiling

Post treatment minimal residual disease (MRD) determination contributes to impending relapse prediction, chemotherapy response and clinical outcomes assessment, guiding clinicians to develop reasonable and eff...

Authors: Ju Bai, Aili He, Wanggang Zhang, Chen Huang, Juan Yang, Yun Yang, Jianli Wang and Yang Zhang

Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction

Cell surface glycoprotein sialylation is one of the most ubiquitous glycan modifications found on higher eukaryotes. The surface sialylation pattern of cells is influenced by the cellular environment but also ...

Authors: Ville I Parviainen, Sakari Joenväärä, Niina Tohmola and Risto Renkonen

Differential protein expression in perfusates from metastasized rat livers

Liver perfusates exhibit theoretical advantages regarding the discovery of disease biomarkers because they contain proteins that readily enter the blood-stream, and perfusion preserves the disease state in its...

Authors: Yang Zhang, Menglin Li, Lilong Wei, Lisi Zhu, Siqi Hu, Shuzhen Wu, Sucan Ma and Youhe Gao

Comparison of first dimension IPG and NEPHGE techniques in two-dimensional gel electrophoresis experiment with cytosolic unfolded protein response in Saccharomyces cerevisiae

Two-dimensional gel electrophoresis (2DE) is one of the most popular methods in proteomics. Currently, most 2DE experiments are performed using immobilized pH gradient (IPG) in the first dimension; however, so...

Authors: Rimantas Slibinskas, Raimundas Ražanskas, Rūta Zinkevičiūtė and Evaldas Čiplys

Erratum to: Heat stress-induced response of the proteomes of leaves from Salvia splendens vista and king

Authors: Hui Liu, Guozheng Shen, Xianping Fang, Qiaojuan Fu, Kangkang Huang, Yi Chen, Hong Yu, HengMu Zhang, Yun Zhao, Le Zhang, Liang Jin and Songlin Ruan

A note on protein expression changes in chicken breast muscle in response to time in transit before slaughtering

Aims of the research were to devise a proteome map of the chicken Pectoralis superficialis muscle, as resolved by two-dimensional gel electrophoresis, and to characterize protein expression changes in the soluble...

Authors: Enrico Zanetti, Antonio Masi, Micaela Pivato, Serena Tolin, Anna Rita Trentin, Cem Guler, Servet Yalçin and Martino Cassandro

A new type of protein chip to detect hepatocellular carcinoma-related autoimmune antibodies in the sera of hepatitis C virus-positive patients

We report here a new type of protein chip to detect antibodies in sera. This chip method was used to a prototype created to detect hepatocellular carcinoma (HCC) -related autoantibodies in the sera of hepatiti...

Authors: Junko Akada, Shuichi Kamei, Akane Ito, Moe Ito, Takao Kitagawa, Hiroko Furumoto, Yukari Kato, Michiko Tamesa, Motonari Takashima, Mutsunori Shirai, Hirofumi Yamano, Masaaki Oka, Yasuhiro Kuramitsu and Kazuyuki Nakamura

Proteomic analysis of the inhibitory effect of epigallocatechin gallate on lipid accumulation in human HepG2 cells

(−)-Epigallocatechin-3-gallate (EGCG), the most abundant catechin found in green tea, effectively reduces body weight and tissue and blood lipid accumulation. To explore the mechanism by which EGCG inhibits ce...

Authors: Zhonghua Liu, Qin Li, Jianan Huang, Qionglin Liang, Yujun Yan, Haiyan Lin, Wenjun Xiao, Yong Lin, Sheng Zhang, Bin Tan and Guoan Luo

Identification of cellular proteome using two-dimensional difference gel electrophoresis in ST cells infected with transmissible gastroenteritis coronavirus

Transmissible gastroenteritis coronavirus (TGEV) is an enteropathogenic coronavirus that causes diarrhea in pigs, which is correlated with high morbidity and mortality in suckling piglets. Information remains ...

Authors: Xin Zhang, Hong-Yan Shi, Jian-Fei Chen, Da Shi, Hong-Wu Lang, Zhong-Tian Wang and Li Feng

Identification of Enolase 1 and Thrombospondin-1 as serum biomarkers in HBV hepatic fibrosis by proteomics

Hepatic fibrosis is an inevitable process in the progression of chronic HBV infection to hepatic cirrhosis, but its detailed mechanism is still unknown. Clinic serum biomarkers of HBV hepatic cirrhosis were sc...

Authors: Bin Zhang, Zi Wang, Bin Deng, Xiaoqiong Wu, Jing Liu and Xueping Feng

Proteomic analyses of age related changes in A.BY/SnJ mouse hearts

A.BY/SnJ mice are used to study pathological alterations in the heart due to enteroviral infections. Since age is a well-known factor influencing the susceptibility of mice to infection, response to stress and...

Authors: Krishnatej Nishtala, Truong Quoc Phong, Leif Steil, Martina Sauter, Manuela Gesell Salazar, Reinhard Kandolf, Stephan B Felix, Uwe Völker, Karin Klingel and Elke Hammer

Comparative secretome analysis of four isogenic Bacillus clausii probiotic strains

The spore-bearing alkaliphilic Bacillus species constitute a large, heterogeneous group of microorganisms, important for their ability to produce enzymes, antibodies and metabolites of potential medical use. Some...

Authors: Rosa Lippolis, Rosa Anna Siciliano, Maria Fiorella Mazzeo, Anna Abbrescia, Antonio Gnoni, Anna Maria Sardanelli and Sergio Papa

Proteomic profiling for the identification of serum diagnostic biomarkers for abdominal and thoracic aortic aneurysms

Aortic aneurysm is an increasingly common vascular disorder with fatal implication. However, there is no established diagnosis other than that based on aneurysmal size. For this purpose, serum protein biomarke...

Authors: Kazumi Satoh, Tomoko Maniwa, Teiji Oda and Ken-ichi Matsumoto

Nuclear proteome response to cell wall removal in rice (Oryza sativa)

Plant cells are routinely exposed to various pathogens and environmental stresses that cause cell wall perturbations. Little is known of the mechanisms that plant cells use to sense these disturbances and tran...

Authors: Hana Mujahid, Feng Tan, Jian Zhang, Babi Ramesh Reddy Nallamilli, Ken Pendarvis and Zhaohua Peng

Heat stress-induced response of the proteomes of leaves from Salvia splendens Vista and King

Salvia splendens Ker-Gawl, most commonly used in China to add a splash of brilliant color to the surroundings during the warm season, is subject to heat stress, which can greatly affect its growth and yield.

Authors: Hui Liu, Guozheng Shen, Xianping Fang, Qiaojuan Fu, Kangkang Huang, Yi Chen, Hong Yu, Yun Zhao, Le Zhang, Liang Jin and Songlin Ruan

Azacytidine induces necrosis of multiple myeloma cells through oxidative stress

Azacytidine is an inhibitor of DNA methyltransferase and is known to be an anti-leukemic agent to induce cancer cell apoptosis. In the present study, multiple myeloma cells were treated with azacytidine at cli...

Authors: Enbing Tian, Haiping Tang, Renhua Xu, Chongdong Liu, Haiteng Deng and Qingtao Wang

Impact of pyrrolidine-bispyrrole DNA minor groove binding agents and chirality on global proteomic profile in Escherichia Coli

There is great interest in the design of small molecules that selectively target minor grooves of duplex DNA for controlling specific gene expression implicated in a disease. The design of chiral small molecul...

Authors: Ya-ting Yang, Chun-Yu Lin, Jingyueh Jeng and Chi-Wi Ong

In-depth mass spectrometric mapping of the human vitreous proteome

Mapping of proteins involved in normal eye functions is a prerequisite to identify pathological changes during eye disease processes. We therefore analysed the proteome of human vitreous by applying in-depth p...

Authors: Sebastian Aretz, Tim U Krohne, Kerstin Kammerer, Uwe Warnken, Agnes Hotz-Wagenblatt, Marion Bergmann, Boris V Stanzel, Tore Kempf, Frank G Holz, Martina Schnölzer and Jürgen Kopitz

Interactions by 2D Gel Electrophoresis Overlap (iGEO): a novel high fidelity approach to identify constituents of protein complexes

Here we describe a novel approach used to identify the constituents of protein complexes with high fidelity, using the integrin-associated scaffolding protein PINCH as a test case. PINCH is comprised of five L...

Authors: Masaaki Yoshigi, Stephen M Pronovost and Julie L Kadrmas

Comparative proteome analysis of Tumor necrosis factor α-stimulated human Vascular Smooth Muscle Cells in response to melittin

Bee venom has been used to relieve pain and to treat inflammatory diseases, including rheumatoid arthritis, in humans. To better understand the mechanisms of the anti-inflammatory and anti-atherosclerosis effe...

Authors: Hyun-Ji Cho, Jeong-Han Kang, Kwan-Kyu Park, Jung-Yoon Choe, Yoon-Yub Park, Yong-Suk Moon, Il-Kyung Chung, Hyeun-Wook Chang, Cheorl-Ho Kim, Yung Hyun Choi, Wun-Jae Kim, Sung-Kwon Moon and Young-Chae Chang

A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: sample preparation, reproducibility, and differential protein expression patterns

Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears...

Authors: Sausan Azzam, Laurie Broadwater, Shuo Li, Ernest J Freeman, Jennifer McDonough and Roger B Gregory