Comparison of three classes of snake neurotoxins by homology modeling and computer simulation graphics

Disorder and cysteines in proteins: A design for orchestration of conformational see-saw and modulatory functions

Being responsible for more than 90% of cellular functions, protein molecules are workhorses in all the life forms. In order to cater for such a high demand, proteins have evolved to adopt diverse structures that allow them to perform myriad of functions. Beginning with the genetically directed amino acid sequence, the classical understanding of protein function involves adoption of hierarchically complex yet ordered structures. However, advances made over the last two decades have revealed that inasmuch as 50% of eukaryotic proteome exists as partially or fully disordered structures. Significance of such intrinsically disordered proteins (IDPs) is further realized from their ability to exhibit multifunctionality, a feature attributable to their conformational plasticity. Among the coded amino acids, cysteines are considered to be "order-promoting" due to their ability to form inter- or intramolecular disulfide bonds, which confer robust thermal stability to the protein structure in oxidizing conditions. The co-existence of order-promoting cysteines with disorder-promoting sequences seems counter-intuitive yet many proteins have evolved to contain such sequences. In this chapter, we review some of the known cysteine-containing protein domains categorized based on the number of cysteines they possess. We show that many protein domains contain disordered sequences interspersed with cysteines. We show that a positive correlation exists between the degree of cysteines and disorder within the sequences that flank them. Furthermore, based on the computational platform, IUPred2A, we show that cysteine-rich sequences display significant disorder in the reduced but not the oxidized form, increasing the potential for such sequences to function in a redox-sensitive manner. Overall, this chapter provides insights into an exquisite evolutionary design wherein disordered sequences with interspersed cysteines enable potential modulatory protein functions under stress and environmental conditions, which thus far remained largely inconspicuous.

Review: protein secondary structure prediction continues to rise

Methods predicting protein secondary structure improved substantially in the 1990s through the use of evolutionary information taken from the divergence of proteins in the same structural family. Recently, the evolutionary information resulting from improved searches and larger databases has again boosted prediction accuracy by more than four percentage points to its current height of around 76% of all residues predicted correctly in one of the three states, helix, strand, and other. The past year also brought successful new concepts to the field. These new methods may be particularly interesting in light of the improvements achieved through simple combining of existing methods. Divergent evolutionary profiles contain enough information not only to substantially improve prediction accuracy, but also to correctly predict long stretches of identical residues observed in alternative secondary structure states depending on nonlocal conditions. An example is a method automatically identifying structural switches and thus finding a remarkable connection between predicted secondary structure and aspects of function. Secondary structure predictions are increasingly becoming the work horse for numerous methods aimed at predicting protein structure and function. Is the recent increase in accuracy significant enough to make predictions even more useful? Because the recent improvement yields a better prediction of segments, and in particular of beta strands, I believe the answer is affirmative. What is the limit of prediction accuracy? We shall see.

Structure-function studies on Taiwan cobra long neurotoxin homolog

A novel long neurotoxin homolog was purified from Naja naja atra (Taiwan cobra) venom using the combination of ion exchange chromatography and reverse phase high performance liquid chromatography. The determined protein sequence was essentially the same as that deduced from the cDNA amplified by reverse transcriptase-polymerase chain reaction. The long neurotoxin homolog exhibited an activity that inhibited acetylcholine-induced muscle contractions, as with N. naja atra cobrotoxin. The degree of inhibition caused by the addition of long neurotoxin homolog was approximately 70% of that observed with the addition of cobrotoxin. Unlike the well-known short and long neurotoxins, this neurotoxin homolog contained two additional cysteine residues forming a disulfide linkage in the N-terminal region. Circular dichroism measurement and computer models of the neurotoxin reveal that its secondary structure was not abundant in beta-sheet as noted with short and long neurotoxins. This less ordered structure may be associated with the lower activity noted with the long neurotoxin homolog. Together with the finding that the known long neurotoxin homologs exclusively appear in the venoms of the Naja and Bungarus genera, the long neurotoxin homologs should represent an evolutionary branch from the long and short neurotoxins in the Elapidae family.

Sequencing and model structure of a Naja naja atra protein fragment

We report the amino acid sequence of a basic protein isolated from the snake venom of Naja naja atra. An automated Edman sequencer was used to determine the 65-residue sequence, aided by electrospray ionization/mass spectrometry. Online reduction and pyridylethylation of the peptide was performed to identify the cysteine residues. Trypsin, chymotrypsin and aspartic digestions were carried out to derive peptide fragments for further sequencing. Fragmented peptides were overlapped to obtain the complete sequence. Molecular mass measurements of the whole protein and its fragments were used as a countercheck for sequence assignment. Further confirmation of the sequence was indicated by sequence homology to other snake venom neurotoxins. A molecular model of the tertiary structure was constructed based on sequence homology, and was refined by global minimization and extensive quality control algorithms. Electrostatic and hydrophobic surface calculations and molecular dynamics simulations were carried out to determine the functional properties of the molecule.