Protein and Peptide Letters - Volume 17, Issue 6, 2010

The sizes of the protein databases are growing rapidly nowadays thus clustering protein sequences based only on sequence information becomes increasingly important. In this paper, we analyze the limitation of Affinity propagation (AP) algorithm when clustering a dataset generated randomly. Then we propose a post-processing method to improve the AP algorithm. This method uses the median of the input similarities as the sh Read More

Lectins, a class of proteins that reversibly and non-enzymatically bind specific sugars, have been purified from different kinds of legumes. In this study, a 48-kDa lectin (KBL) was purified from Korean large black soybeans using liquid chromatography. The specific hemagglutinating activity of the KBL was 4096 titer/mg. EDTA-induced loss of hemagglutinating activity of KBL could be recovered by addition of Fe3+ ions and som Read More

An all-atom level MD simulation in explicit solvent at high temperature is a powerful technique to increase our knowledge about the structurally important regions modulating thermal stability in thermoenzymes. In this respect, two large-sized thermoalkalophilic enzymes from Bacillus stearothermophilus L1 (L1 lipase) and Geobacillus zalihae strain T1 (T1 lipase) are well-established representatives. In this paper, compa Read More

Four AS-48 mutants (Trp24Ala, Gly13Lys, Leu40Lys and Ala53Ser) were obtained by site-directed mutagenesis. The minimal inhibitory concentration of each peptide showed that only residue Trp24 was unquestionably involved in the biological activity. Guanidine hydrochloride-induced unfolding assays showed a three-state transition denaturation process, suggesting a molten-globule-like conformation after the first transition.

The early determination of family for a newly found enzyme molecule becomes important because it is directly related to the detail information about which specific target it acts on, as well as to its catalytic process and biological function. Unfortunately, it is still a hard work to distinguish enzyme classes by experiments. With an enormous amount of protein sequences uncovered in the genome research, it is both challengi Read More

State-of-the-art biochemistry methods in combination with an automated phenotyping method demonstrate the high potential of transgenic tobacco plants in producing properly-folded therapeutic proteins for the treatment of protein-misfolding diseases (e.g., Alzheimer's disease). This molecular farming approach led to highest protein production of hydroponically- grown tobacco compared to other growth substrates g Read More

Mitogen-activated protein kinases (MAPKs) are key components of cellular signal transduction. It is the objective of this communication to demonstrate that insight into protein-protein interactions in the Common Docking motif of yeast mitogen-activated protein kinases can be obtained based on homology models. Homology models for four yeast MAPKs, FUS3, KSS1, HOG1 and MPK1 were built based on the X-ray structu Read More

In this paper, we report our study of thermodynamic parameters of the interactions of antifreeze proteins (AFP) type I and it short segments with DMPC unilamellar vesicles as model for cell membrane. The heat of interactions between AFP's and the model cell membrane were studied by Isothermal Titration Calorimetry (ITC) at temperatures above and below phase transition temperatures of the membrane. It is shown th Read More

MSH proteins are capable of recognizing damage in DNA due to a common chemotheraputic, cisplatin, and consequently participate in the initiation of cell death pathways. While previous studies have used computational modeling and cell biology to demonstrate that there are specific structural responses to cisplatin damage that are critical to the initiation of apoptosis, this study demonstrates that there are also specific dynamic Read More

SsHSP14.1, a novel sHSP from the hyper-thermophilic archaeon Sulfolobus solfataricus (S. solfataricus), is reported herein to function to protect EcoR I from heat-induced inactivation. A predicted salt bridge and hydrophobic interactions were found to be important for this function.

The coupling of an aspartate residue with an active site histidine plays a pivotal role in enzyme catalysis. The His-Asp pair in glutamate mutase and other B12-dependent mutases is not only responsible for coenzyme-binding, but is also involved in fine-tuning the enzymatic activities. Our modeling results show that the His-Asp pair is arranged in a highly organized manner. Except for carboxymethylated Cys or Glu, a less hi Read More

In this study, we have developed a standalone tool called as ANAMBS (Analysis of Metal Binding Site) to derive metal neighbourhood information using PERL as the programming language. The tool accepts the structures in the pdb format. The cut off distance to define the metal binding region can be specified. The metal binding site composition, orientation of various amino acids and atoms along with the Hydropathy index with Read More

Shigella dysenteriae type 1 and Escherichia coli O157:H7 produce Shiga toxin (Stx) and Shiga toxin (Stx1), respectively and these two toxins are almost identical. E. coli O157:H7 is the major cause of diarrhea-associated hemolytic uremic syndrome. Stx and Stx1 are AB5 type of toxin with a molecular weight of 70 kDa, comprising an enzymaticalyactive A subunit (32 kDa) and five receptor-binding B subunits (7.7 kDa). In this Read More

A 26-kDa trypsin inhibitor with an N-terminal sequence resembling storage proteins was purified from moth beans (Phaseolus acutifolius). It dose-dependently inhibited trypsin with an IC50 value of about 0.38 μM. It inhibited [methyl-3H] thymidine incorporation by lymphoma MBL2 cells with an IC50 value of 20 μM.

The prediction of protein function is a difficult and important problem in computational biology. In this study, an efficient method is presented to predict protein function with sequence composition information. Four kinds of basic building blocks of protein sequences are investigated, including N-grams, binary profiles, PFAM domains and InterPro domains. The protein sequences are mapped into high-dimensional vectors by usin Read More

Enzyme-substrate interaction under the presence of high concentration of salts is of great interest for biotechnology applications and basic enzymology. In our previous work, the salt effect on halophilic subtilase SR5-3 was evaluated with Suc-AAPF-MCA and with the FRET peptide Abz-AAPFSSKQ-EDDnp. It was demonstrated that the magnitude of catalytic activity enhancement was affected by the presence of the prim Read More

A novel exo-glucanase gene (xeg5B) was isolated from a rumenal microbial metagenome, cloned, and expressed in E. coli. The 1548 bp gene coded for a protein of 516 amino acids, which assumed an (α/β)8 fold typical of glycoside hydrolase (GH) family 5. The protein molecule consisted of a loop segment blocking one end of the active site, which potentially provided the enzyme with exo-acting property. The recombinant Read More