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Role of large hydrophobic residues in proteins
Veerasamy Jayaraj,Ramamoorthi Suhanya,Marimuthu Vijayasarathy,Perumal Anandagopu
Bioinformation , 2009,
Abstract: Large Hydrophobic Residues (LHR) such as phenylalanine, isoleucine, leucine, methionine and valine play an important role in protein structure and activity. We describe the role of LHR in complete set of protein sequences in 15 different species. That is the distribution of LHR in different proteins of different species is reported. It is observed that the proteins prefer to have 27% of large hydrophobic residues in total and all along the sequence. It is also observed that proteins accumulate more LHR in its active sites. A window analysis on these protein sequences shows that the 27% of LHR is more frequent at window length of 45 amino acids. The influenza virus and P. falciparum show a random distribution of LHR in its proteins compared to other model organisms.
Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling
Benoit Adam, Benoit Charloteaux, Jerome Beaufays, Luc Vanhamme, Edmond Godfroid, Robert Brasseur, Laurence Lins
BMC Structural Biology , 2008, DOI: 10.1186/1472-6807-8-1
Abstract: The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure. Under the 30% identity threshold, alignment methods do not correctly assign and align proteins. The only safe way to assign a sequence to that family is by experimental determination. However, these procedures are long and costly and cannot always be applied. A way to circumvent the experimental approach is sequence and structure analyze. To further help in that task, the residues implicated in the stabilisation of the lipocalin fold were determined. This was done by analyzing the conserved interactions for ten lipocalins having a maximum pairwise identity of 28% and various functions.It was determined that two hydrophobic clusters of residues are conserved by analysing the ten lipocalin structures and sequences. One cluster is internal to the barrel, involving all strands and the 310 helix. The other is external, involving four strands and the helix lying parallel to the barrel surface. These clusters are also present in RaHBP2, a unusual "outlier" lipocalin from tick Rhipicephalus appendiculatus. This information was used to assess assignment of LIR2 a protein from Ixodes ricinus and to build a 3D model that helps to predict function. FTIR data support the lipocalin fold for this protein.By sequence and structural analyzes, two conserved clusters of hydrophobic residues in interactions have been identified in lipocalins. Since the residues implicated are not conserved for function, they should provide the minimal subset necessary to confer the lipocalin fold. This information has been used to assign LIR2 to lipocalins and to investigate its structure/function relationship. This study could be applied to other protein families with low pairwise similarity, such as the structurally related fatty acid binding proteins or avidins.Lipocalins are small secreted proteins (160–200 residues), typically structured in a 8 strands up and down β-barrel. A 310
Protein contact networks at different length scales and role of hydrophobic, hydrophilic and charged residues in protein's structural organisation  [PDF]
Dhriti Sengupta,Sudip Kundu
Quantitative Biology , 2010,
Abstract: The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed protein contact networks at different length scales, long and short-range. While long and short-range interactions are determined by the positions of amino acids in primary chain, the contact networks are constructed based on the 3D spatial distances of amino acids. We have further divided these networks into sub-networks of hydrophobic, hydrophilic and charged residues. Our analysis reveals that a significantly higher percentage of assortative sub-clusters of long-range hydrophobic networks helps a protein in communicating the necessary information for protein folding in one hand; on the other hand the higher values of clustering coefficients of hydrophobic sub-clusters play a major role in slowing down the process so that necessary local and global stability can be achieved through intra connectivities of the amino acid residues. Further, higher degrees of hydrophobic long-range interactions suggest their greater role in protein folding and stability. The small-range all amino acids networks have signature of hierarchy. The present analysis with other evidences suggest that in a protein's 3D conformational space, the growth of connectivity is not evolved either through preferential attachment or through random connections; rather, it follows a specific structural necessity based guiding principle - where some of the interactions are primary while the others, generated as a consequence of these primary interactions are secondary.
Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information
Peng Chen, Jinyan Li
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-402
Abstract: We propose a new idea to construct an integrative profile for each residue in a protein by combining its hydrophobic and evolutionary information. A support vector machine (SVM) ensemble is then developed, where SVMs train on different pairs of positive (interface sites) and negative (non-interface sites) subsets. The subsets having roughly the same sizes are grouped in the order of accessible surface area change before and after complexation. A self-organizing map (SOM) technique is applied to group similar input vectors to make more accurate the identification of interface residues. An ensemble of ten-SVMs achieves an MCC improvement by around 8% and F1 improvement by around 9% over that of three-SVMs. As expected, SVM ensembles constantly perform better than individual SVMs. In addition, the model by the integrative profiles outperforms that based on the sequence profile or the hydropathy scale alone. As our method uses a small number of features to encode the input vectors, our model is simpler, faster and more accurate than the existing methods.The integrative profile by combining hydrophobic and evolutionary information contributes most to the protein-protein interaction prediction. Results show that evolutionary context of residue with respect to hydrophobicity makes better the identification of protein interface residues. In addition, the ensemble of SVM classifiers improves the prediction performance.Datasets and software are available at http://mail.ustc.edu.cn/~bigeagle/BMCBioinfo2010/index.htm webcite.In living cells, proteins interact with other proteins in order to perform specific biological functions, such as signal transduction or immunological recognition, DNA replication and gene translation, as well as protein synthesis [1]. These interactions are localized to the so-called "interaction sites" or "interface residues".Identification of these residues will allow us to understand how proteins recognize other molecules and to gain clues into their po
Inconsistent Distances in Substitution Matrices can be Avoided by Properly Handling Hydrophobic Residues
J. Baussand,A. Carbone
Evolutionary Bioinformatics , 2008,
Abstract: The adequacy of substitution matrices to model evolutionary relationships between amino acid sequences can be numerically evaluated by checking the mathematical property of triangle inequality for all triplets of residues. By converting substitution scores into distances, one can verify that a direct path between two amino acids is shorter than a path passing through a third amino acid in the amino acid space modeled by the matrix. If the triangle inequality is not verified, the intuition is that the evolutionary signal is not well modeled by the matrix, that the space is locally inconsistent and that the matrix construction was probably based on insufficient biological data. Previous analysis on several substitution matrices revealed that the number of triplets violating the triangle inequality increases with sequence divergence. Here, we compare matrices which are dedicated to the alignment of highly divergent proteins. The triangle inequality is tested on several classical substitution matrices as well as in a pair of “complementary” substitution matrices recording the evolutionary pressures inside and outside hydrophobic blocks in protein sequences. The analysis proves the crucial role of hydrophobic residues in substitution matrices dedicated to the alignment of distantly related proteins.
Mutation of exposed hydrophobic amino acids to arginine to increase protein stability
Caroline Strub, Carole Alies, Andrée Lougarre, Caroline Ladurantie, Jerzy Czaplicki, Didier Fournier
BMC Biochemistry , 2004, DOI: 10.1186/1471-2091-5-9
Abstract: In order to test it, we replaced 14 solvent-exposed hydrophobic residues of acetylcholinesterase by arginine. The stabilities of the resulting proteins were tested using denaturation by high temperature, organic solvents, urea and by proteolytic digestion.Altough the mutational effects were rather small, this strategy proved to be successful since half of the mutants showed an increased stability. This stability may originate from the suppression of unfavorable interactions of nonpolar residues with water or from addition of new hydrogen bonds with the solvent. Other mechanisms may also contribute to the increased stability observed with some mutants. For example, introduction of a charge at the surface of the protein may provide a new coulombic interaction on the protein surface.Acetylcholinesterase (AChE, EC is a serine hydrolase, which catalyzes the hydrolysis of the neurotransmitter acetylcholine. This enzyme is irreversibly inhibited by organophosphate and carbamate pesticides leading to its use in biosensors to detect traces of these compounds in environment. Drosophila AChE was found to be the most sensitive enzyme when compared to enzymes of non-insect origin and in-vitro-mutagenesis was used to select enzymes up to 300-fold more sensitive [1,2]. But like most enzymes from mesophilic organisms, Drosophila AChE is not stable, and this instability precludes its utilization in biosensors. It can be stabilized by adding some molecules in the solution such as reversible inhibitors, polyethylene glycol or protein, provoking protein-protein interactions. Alternatively, stabilization may also be achieved by encapsulation in liposomes [3,7]. Another way to stabilize the enzyme is to use in vitro mutagenesis to modify the primary structure of the protein [8]. This method could have the additional advantage of stabilizing the enzyme during its synthesis leading to higher production and higher purification yields.Irreversible denaturation of AChE at room temper
"Hot cores" in proteins: Comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms
Alessandro Paiardini, Riccardo Sali, Francesco Bossa, Stefano Pascarella
BMC Structural Biology , 2008, DOI: 10.1186/1472-6807-8-14
Abstract: The construction of two datasets was carried out so as to satisfy several restrictive criteria, such as minimum redundancy, resolution and R-value thresholds and lack of any structural defect in the collected structures. This approach allowed to quantify with relatively high precision the apolar contact area between interacting residues, reducing the uncertainty due to the position of atoms in the crystal structures, the redundancy of data and the size of the dataset. To identify the common core regions of these proteins, the study was focused on segments that conserve a similar main chain conformation in the structures analyzed, excluding the intervening regions whose structure differs markedly. The results indicated that hyperthermophilic proteins underwent a significant increase of the hydrophobic contact area contributed by those residues composing the alpha-helices of the structurally conserved regions.This study indicates the decreased flexibility of alpha-helices in proteins core as a major factor contributing to the enhanced termostability of a number of hyperthermophilic proteins. This effect, in turn, may be due to an increased number of buried methyl groups in the protein core and/or a better packing of alpha-helices with the rest of the structure, caused by the presence of hydrophobic beta-branched side chains.Earth's environments exhibit the most diverse physico-chemical conditions, including extremes of temperature, pressure, salinity and pH. Among these factors, temperature certainly exerts a deep selective pressure on cell biochemistry and physiology [1]. Indeed, temperatures approaching 100°C usually denature proteins and nucleic acids, and increase the fluidity of membranes to lethal levels [2]. It is therefore of great interest to study how organisms coped with the molecular adaptations required to thrive in extreme environments, particularly at high temperatures. Such organisms, which are distributed among the three domains of life, are called "t
A Comparative Study of the Second-Order Hydrophobic Moments for Globular Proteins: The Consensus Scale of Hydrophobicity and the CHARMM Partial Atomic Charges  [PDF]
Cheng-Fang Tsai,Kuei-Jen Lee
International Journal of Molecular Sciences , 2011, DOI: 10.3390/ijms12128449
Abstract: In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues ( N) and the asphericity ( δ). Proteins in Group I were spherical and those in Groups II and III were prolate. The size of the proteins is represented by the mean radius of gyration ( R g), which follows the Flory scaling law, R g ∝ Nv. The mean value of v was 0.35, which is similar to a polymer chain in a poor solvent. The spatial distributions of the second-order moment for each of the proteins, obtained from the two sets of hydrophobicity, were compared using the Pearson correlation coefficient; the results reveal that there is a strong correlation between the two data sets for each protein structure when the CHARMM partial atomic charges, | qi|? ≥ 0.3, assigned for polar atoms, are used. The locations at which these distributions vanish and approach a negative value are at approximately 50% of the percentage of solvent accessibility, indicating that there is a transition point from hydrophobic interior to hydrophilic exterior in the proteins. This may suggest that there is a position for the proteins to determine the residues at exposed sites beyond this range.
Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization
Dhriti Sengupta, Sudip Kundu
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-142
Abstract: The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don’t. While the nature of transitions of LCC’s sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at higher interaction strength between amino acids, give extra stability to the tertiary structure of the thermophiles. All the subnetworks at different length scales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids. While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs and LRNs; we do not find the assortative mixing behaviour of any the subclusters in SRNs. The clustering coefficient of hydrophobic subclusters in long-range network is the highest among types of subnetworks. There exist highly cliquish hydrophobic nodes followed by charged nodes in LRNs and ARNs; on the other hand, we observe the highest dominance of charged residues cliques in short-range networks. Studies on the perimeter of the cliques also show higher occurrences of hydrophobic and charged residues’ cliques.The simple framework of protein contact networks and their subnetworks based on London van der Waals force is able to capture several known properties of protein structure as well as can unravel several new features. Th
Fall and rise of small droplets on rough hydrophobic substrates  [PDF]
Markus Gross,Fathollah Varnik,Dierk Raabe
Physics , 2009, DOI: 10.1209/0295-5075/88/26002
Abstract: Liquid droplets on patterned hydrophobic substrates are typically observed either in the Wenzel or the Cassie state. Here we show that for droplets of comparable size to the roughness scale an additional local equilibrium state exists, where the droplet is immersed in the texture, but not yet contacts the bottom grooves. Upon evaporation, a droplet in this state enters the Cassie state, leading to a qualitatively new self-cleaning mechanism. The effect is of generic character and is expected to occur in any hydrophobic capillary wetting situation where a spherical liquid reservoir is involved.
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