Recent studies show that the common paradigm of sequence to structure to function is insufficient for understanding the mechanisms of biomolecular interactions and functions. Protein structures are dynamic rather than static, and it’s the protein's dynamics that plays a key role in a wide range of biological activities such as binding, allosteric signaling, and transporting. Thus, developing novel algorithms that are able to compare the dynamics of proteins with different length and structure are expected to open up new horizons toward understanding the dynamics to function relationship of proteins.We develop novel algorithms that can compare the dynamics of proteins even without any apparent sequence or structural similarity. Algorithms such as the Needleman–Wunsch (global alignment) and the Needleman–Wunsch (local alignment) that are commonly used for aligning two protein sequences are modified by us for aligning Normal Mode Analysis proteins’ modes of motions. The newly developed algorithms allow us to examine the effects such as allosteric effectors and quaternary structure on protein dynamics.
The dynamics of the ligand-binding domain (LBD) and the intact ionotropic glutamate receptor (iGl... more The dynamics of the ligand-binding domain (LBD) and the intact ionotropic glutamate receptor (iGluR) were studied using Gaussian Network Model (GNM) analysis. The dynamics of LBDs with various allosteric modulators is compared using a novel method of multiple alignment of GNM modes of motion. The analysis reveals that allosteric effectors change the dynamics of amino acids at the upper lobe interface of the LBD dimer as well as at the hinge region between the upper- and lower- lobes. For the intact glutamate receptor the analysis show that the clamshell-like movement of the LBD upper and lower lobes is coupled to the bending of the trans-membrane domain (TMD) helices which may open the channel pore. The results offer a new insight on the mechanism of action of allosteric modulators on the iGluR and support the notion of TMD helices bending as a possible mechanism for channel opening. In addition, the study validates the methodology of multiple GNM modes alignment as a useful tool to...
Expression of the N-type voltage sensitive calcium channel in Xenopus oocytes along with syntaxin... more Expression of the N-type voltage sensitive calcium channel in Xenopus oocytes along with syntaxin and p65 showed that the syntaxin-modified N-type channel properties, were fully reversed by p65. The inward current was restored to a significantly higher amplitude when all three proteins were present, suggesting that the channel interacts with syntaxin, p65 and SNAP-25 in a quaternary complex. Further support to a multicomplex formation between the channel and the synaptic proteins was drawn from the steady-state voltage inactivation profiles. A physical interaction of the N-type calcium channel with the vesicular protein synaptotagmin (p65) was demonstrated biochemically, using recombinant fusion proteins. The interaction is confined to a cytosolic channel domain that separates segments II and III amino acids 710-1090 of the N-type channel (N-Loop710-1090). In vitro binding of recombinant N-Loop710-1090 to p65 (amino acids 96-421) involves the two C2 domains of p65, C2A domain [amino...
Annotation of the rapidly accumulating body of sequence ,data relies heavily on the ,detection of... more Annotation of the rapidly accumulating body of sequence ,data relies heavily on the ,detection of remote Abstract homologues,and functional motifs in protein families. The most popular methods rely on sequence alignment. These include programs that use a scoring matrix to compare ,the probability of a potential alignment with random,chance and programs that use curated multiple alignments to train profile hidden
Gaussian network model (GNM) modes of motion are calculated to a dataset of hemoglobin (Hb) struc... more Gaussian network model (GNM) modes of motion are calculated to a dataset of hemoglobin (Hb) structures and modes with dynamics similarity to the T state are multiply aligned. The sole criterion for the alignment is the mode shape itself and not sequence or structural similarity. Standard deviation (SD) of the GNM value score along the alignment is calculated, regions with high SD are defined as dynamically variable. The analysis shows that the α1β1/α2β2 interface is a dynamically variable region but not the α1β2/α2β1 and the α1α2/β1β2 interfaces. The results are in accordance with the T→R2 transition of Hb. We suggest that dynamically variable regions are regions that are likely to undergo structural change in the protein upon binding, conformational transition, or any other relevant chemical event. The represented technique of multiple dynamics-based alignment of modes is novel and may offer a new insight in proteins' dynamics to function relation.
Proteins: Structure, Function, and Bioinformatics, 2012
A novel methodology for comparison of protein dynamics is presented. Protein dynamics is calculat... more A novel methodology for comparison of protein dynamics is presented. Protein dynamics is calculated using the Gaussian network model and the modes of motion are globally aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. The alignment is fast and can be used to analyze large sets of proteins. The methodology is applied to the four major classes of the SCOP database: "all alpha proteins," "all beta proteins," "alpha and beta proteins," and "alpha/beta proteins". We show that different domains may have similar global dynamics. In addition, we report that the dynamics of "all alpha proteins" domains are less specific to structural variations within a given fold or superfamily compared with the other classes. We report that domain pairs with the most similar and the least similar global dynamics tend to be of similar length. The significance of the methodology is that it suggests a new and efficient way of mapping between the global structural features of protein families/subfamilies and their encoded dynamics.
ABSTRACT Sequence and structure comparisons are fundamental techniques that enable exploration of... more ABSTRACT Sequence and structure comparisons are fundamental techniques that enable exploration of the sequence and structural spaces of proteins. Homology detection, function prediction, and protein classification rely on these techniques. However, protein structures are dynamic, rather than static, and such protein dynamics play a key role in a wide range of biological activities. Therefore, protein dynamics comparison algorithms may shed light on the relationship between proteins′ dynamics and function. Here, we review different strategies for comparing dynamics of proteins. Special emphasis is given to newly developed algorithms that compare dynamics of proteins with no apparent sequence or structural similarity and to the qualitative differences between these algorithms.
The dynamics of the ligand-binding domain (LBD) and the intact ionotropic glutamate receptor (iGl... more The dynamics of the ligand-binding domain (LBD) and the intact ionotropic glutamate receptor (iGluR) were studied using Gaussian Network Model (GNM) analysis. The dynamics of LBDs with various allosteric modulators is compared using a novel method of multiple alignment of GNM modes of motion. The analysis reveals that allosteric effectors change the dynamics of amino acids at the upper lobe interface of the LBD dimer as well as at the hinge region between the upper- and lower- lobes. For the intact glutamate receptor the analysis show that the clamshell-like movement of the LBD upper and lower lobes is coupled to the bending of the trans-membrane domain (TMD) helices which may open the channel pore. The results offer a new insight on the mechanism of action of allosteric modulators on the iGluR and support the notion of TMD helices bending as a possible mechanism for channel opening. In addition, the study validates the methodology of multiple GNM modes alignment as a useful tool to...
Expression of the N-type voltage sensitive calcium channel in Xenopus oocytes along with syntaxin... more Expression of the N-type voltage sensitive calcium channel in Xenopus oocytes along with syntaxin and p65 showed that the syntaxin-modified N-type channel properties, were fully reversed by p65. The inward current was restored to a significantly higher amplitude when all three proteins were present, suggesting that the channel interacts with syntaxin, p65 and SNAP-25 in a quaternary complex. Further support to a multicomplex formation between the channel and the synaptic proteins was drawn from the steady-state voltage inactivation profiles. A physical interaction of the N-type calcium channel with the vesicular protein synaptotagmin (p65) was demonstrated biochemically, using recombinant fusion proteins. The interaction is confined to a cytosolic channel domain that separates segments II and III amino acids 710-1090 of the N-type channel (N-Loop710-1090). In vitro binding of recombinant N-Loop710-1090 to p65 (amino acids 96-421) involves the two C2 domains of p65, C2A domain [amino...
Annotation of the rapidly accumulating body of sequence ,data relies heavily on the ,detection of... more Annotation of the rapidly accumulating body of sequence ,data relies heavily on the ,detection of remote Abstract homologues,and functional motifs in protein families. The most popular methods rely on sequence alignment. These include programs that use a scoring matrix to compare ,the probability of a potential alignment with random,chance and programs that use curated multiple alignments to train profile hidden
Gaussian network model (GNM) modes of motion are calculated to a dataset of hemoglobin (Hb) struc... more Gaussian network model (GNM) modes of motion are calculated to a dataset of hemoglobin (Hb) structures and modes with dynamics similarity to the T state are multiply aligned. The sole criterion for the alignment is the mode shape itself and not sequence or structural similarity. Standard deviation (SD) of the GNM value score along the alignment is calculated, regions with high SD are defined as dynamically variable. The analysis shows that the α1β1/α2β2 interface is a dynamically variable region but not the α1β2/α2β1 and the α1α2/β1β2 interfaces. The results are in accordance with the T→R2 transition of Hb. We suggest that dynamically variable regions are regions that are likely to undergo structural change in the protein upon binding, conformational transition, or any other relevant chemical event. The represented technique of multiple dynamics-based alignment of modes is novel and may offer a new insight in proteins' dynamics to function relation.
Proteins: Structure, Function, and Bioinformatics, 2012
A novel methodology for comparison of protein dynamics is presented. Protein dynamics is calculat... more A novel methodology for comparison of protein dynamics is presented. Protein dynamics is calculated using the Gaussian network model and the modes of motion are globally aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. The alignment is fast and can be used to analyze large sets of proteins. The methodology is applied to the four major classes of the SCOP database: "all alpha proteins," "all beta proteins," "alpha and beta proteins," and "alpha/beta proteins". We show that different domains may have similar global dynamics. In addition, we report that the dynamics of "all alpha proteins" domains are less specific to structural variations within a given fold or superfamily compared with the other classes. We report that domain pairs with the most similar and the least similar global dynamics tend to be of similar length. The significance of the methodology is that it suggests a new and efficient way of mapping between the global structural features of protein families/subfamilies and their encoded dynamics.
ABSTRACT Sequence and structure comparisons are fundamental techniques that enable exploration of... more ABSTRACT Sequence and structure comparisons are fundamental techniques that enable exploration of the sequence and structural spaces of proteins. Homology detection, function prediction, and protein classification rely on these techniques. However, protein structures are dynamic, rather than static, and such protein dynamics play a key role in a wide range of biological activities. Therefore, protein dynamics comparison algorithms may shed light on the relationship between proteins′ dynamics and function. Here, we review different strategies for comparing dynamics of proteins. Special emphasis is given to newly developed algorithms that compare dynamics of proteins with no apparent sequence or structural similarity and to the qualitative differences between these algorithms.
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Papers by Dror Tobi