Contents Detailed Methods 2 Supplementary Table 5 (2009)
Illés J Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N
basis of signal integration in the transcriptionalregulatory
3.1.2 Functional Motions of Proteins Are Cooperative (2008)
A. J. Rader, Chakra Chennubhotla, Lee-wei Yang, Ivet Bahar
Structure and Function.............................................. 43
Yoram Vodovotz, Elife Zerrin Bagci, G. Bard Ermentrout, Carson C. Chow, Ivet Bahar, ...
Abstract: Nitric oxide (NO•) and its reaction products are key players in the physiology and pathophysiology of inflammatory settings such as sepsis and shock. The consequences of the expression of...
Analysis of correlated mutations in HIV-1 protease using spectral clustering (2008)
Liu, Ying, Eyal, Eran, Bahar, Ivet
Motivation: The ability of human immunodeficiency virus-1 (HIV-1) protease to develop mutations that confer multi-drug resistance (MDR) has been a major obstacle in designing rational therapies...
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations (2007)
Chakra Chennubhotla, Ivet Bahar
Elastic network (EN) models have been widely used in recent years for describing protein dynamics, based on the premise that the motions naturally accessible to native structures are relevant to...
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices (2007)
Eyal, Eran, Pietrokovski, Shmuel, Bahar, Ivet
Identification of correlated amino acids in proteins has been a topic of broad interest in view of its functional implications and importance in protein design. A new set of pair-to-pair (P2P)...
Abstract Background A wealth of unannotated and functionally unknown protein sequences has accumulated in recent years with rapid progresses in sequence genomics, giving rise to ever increasing...
1 Markov Methods for Protein Dynamics (2007)
Prof Ivet Bahar, Chakra Chennubhotla, Ivet Bahar
Elastic network models (ENMs), and in particular the Gaussian Network Model (GNM), have been widely used in recent years to gain insights into the machinery of proteins. The extension of ENMs to...
Farkas, Illes J., Wu, Chuang, Chennubhotla, Chakra, Bahar, Ivet, Oltvai, Zoltan N.
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response...
Farkas, Illés J, Wu, Chuang, Chennubhotla, Chakra, Bahar, Ivet, Oltvai, Zoltán N
Abstract Background Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in...
Markov methods for hierarchical coarse-graining (2006)
Chakra Chennubhotla, Ivet Bahar
Elastic network models (ENMs) and, in particular, the Gaussian Network Model (GNM) have been widely used in recent years to gain insights into the machinery of proteins. The extension of ENMs to...
Anisotropic network model: systematic evaluation and a new web interface (2006)
Eran Eyal, Lee-wei Yang, Ivet Bahar, Anna Tramontano
Motivation: The Anisotropic Network Model (ANM) is a simple yet powerful model for Normal Mode Analysis of proteins. Despite its broad use for exploring biomolecular collective motions, ANM has not...
oGNM: online computation of structural dynamics using the Gaussian Network Model (2006)
Yang, Lee-Wei, Rader, A. J., Liu, Xiong, Jursa, Cristopher Jon, Chen, Shann Ching, Karimi, Hassan A., ...
An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards...
Anisotropic network model: systematic evaluation and a new web interface (2006)
Eyal, Eran, Yang, Lee-Wei, Bahar, Ivet
Motivation: The Anisotropic Network Model (ANM) is a simple yet powerful model for normal mode analysis of proteins. Despite its broad use for exploring biomolecular collective motions, ANM has not...
iGNM: a database of protein functional motions based on Gaussian Network Model (2005)
Yang, Lee-Wei, Liu, Xiong, Jursa, Christopher J., Holliman, Mark, Rader, A. J., Karimi, Hassan A., ...
Motivation: Knowledge of structure is not sufficient for understanding and controlling protein function. Function is a dynamic property. While protein structural information has been rapidly...
A Sequence Alignment-Independent Method for Protein Classification (2004)
John K. Vries, Rajan Munshi, Dror Tobi, Judith Klein-seetharaman, Panayiotis V. Benos, Ivet Bahar
Annotation of the rapidly accumulating body of sequence data relies heavily on the detection of remote homologues and functional motifs in protein families. The most popular methods rely on sequence...
Mining frequent patterns in protein structures: a study of protease families (2004)
Chen, Shann-Ching, Bahar, Ivet
Motivation: Analysis of protein sequence and structure databases usually reveal frequent patterns (FP) associated with biological function. Data mining techniques generally consider the...
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model (2002)
Ozkan, S. Banu, Dill, Ken A., Bahar, Ivet
Do two-state proteins fold by pathways or funnels? Native-state hydrogen exchange experiments show discrete nonnative structures in equilibrium with the native state. These could be called hidden...
Cooperative fluctuations and subunit communication in tryptophan synthase (1999)
Ivet Bahar, Robert L. Jernigan
ABSTRACT: Tryptophan synthase (TRPS), with linearly arrayed subunits R��R, catalyzes the last two reactions in the biosynthesis of L-tryptophan. The two reactions take place in the respective R-...
Identification of core amino acids stabilizing rhodopsin
Rader, A. J., Anderson, Gülsüm, Isin, Basak, Khorana, H. Gobind, Bahar, Ivet, Klein-Seetharaman, Judith
Rhodopsin is the only G protein-coupled receptor (GPCR) whose 3D structure is known; therefore, it serves as a prototype for studies of the GPCR family of proteins. Rhodopsin dysfunction has been...
High-efficiency bypass of DNA damage by human DNA polymerase Q
Seki, Mineaki, Masutani, Chikahide, Yang, Lee Wei, Schuffert, Anthony, Iwai, Shigenori, Bahar, Ivet, ...
Endogenous DNA damage arises frequently, particularly apurinic (AP) sites. These must be dealt with by cells in order to avoid genotoxic effects. DNA polymerase θ is a newly identified enzyme...
Sluis-Cremer, Nicolas, Temiz, N. Alpay, Bahar, Ivet
Nonnucleoside reverse transcriptase inhibitors (NNRTI) are a group of small hydrophobic compounds with diverse structures that specifically inhibit HIV-1 reverse transcriptase (RT). NNRTIs interact...
Functional motions of influenza virus hemagglutinin: a structure-based analytical approach.
Isin, Basak, Doruker, Pemra, Bahar, Ivet
Influenza virus hemagglutinin (HA), a homotrimeric integral membrane glycoprotein essential for viral infection, is engaged in two biological functions: recognition of target cells' receptor proteins...
Relating molecular flexibility to function: a case study of tubulin.
Keskin, Ozlem, Durell, Stewart R, Bahar, Ivet, Jernigan, Robert L, Covell, David G
Microtubules (MT), along with a variety of associated motor proteins, are involved in a range of cellular functions including vesicle movement, chromosome segregation, and cell motility. MTs are...
Maturation Dynamics of Bacteriophage HK97 Capsid
Rader, A.J., Vlad, Daniel H., Bahar, Ivet
Maturation of the bacteriophage HK97 capsid requires a large conformational change of the virus capsid. Experimental studies have identified several intermediates along this maturation pathway. To...
Protein–protein binding usually involves structural changes that may extend beyond the rearrangements on a local scale, and cannot be explained by a classical lock-and-key mechanism. Several models...
oGNM: online computation of structural dynamics using the Gaussian Network Model
Yang, Lee-Wei, Rader, A. J., Liu, Xiong, Jursa, Cristopher Jon, Chen, Shann Ching, Karimi, Hassan A., ...
An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards...
Identification of core amino acids stabilizing rhodopsin
Rader, A. J., Anderson, Gülsüm, Isin, Basak, Khorana, H. Gobind, Bahar, Ivet, Klein-Seetharaman, Judith
Rhodopsin is the only G protein-coupled receptor (GPCR) whose 3D structure is known; therefore, it serves as a prototype for studies of the GPCR family of proteins. Rhodopsin dysfunction has been...
High-efficiency bypass of DNA damage by human DNA polymerase Q
Seki, Mineaki, Masutani, Chikahide, Yang, Lee Wei, Schuffert, Anthony, Iwai, Shigenori, Bahar, Ivet, ...
Endogenous DNA damage arises frequently, particularly apurinic (AP) sites. These must be dealt with by cells in order to avoid genotoxic effects. DNA polymerase θ is a newly identified enzyme...
Functional motions of influenza virus hemagglutinin: a structure-based analytical approach.
Isin, Basak, Doruker, Pemra, Bahar, Ivet
Influenza virus hemagglutinin (HA), a homotrimeric integral membrane glycoprotein essential for viral infection, is engaged in two biological functions: recognition of target cells' receptor proteins...
Relating molecular flexibility to function: a case study of tubulin.
Keskin, Ozlem, Durell, Stewart R, Bahar, Ivet, Jernigan, Robert L, Covell, David G
Microtubules (MT), along with a variety of associated motor proteins, are involved in a range of cellular functions including vesicle movement, chromosome segregation, and cell motility. MTs are...
Protein–protein binding usually involves structural changes that may extend beyond the rearrangements on a local scale, and cannot be explained by a classical lock-and-key mechanism. Several models...
oGNM: online computation of structural dynamics using the Gaussian Network Model
Yang, Lee-Wei, Rader, A. J., Liu, Xiong, Jursa, Cristopher Jon, Chen, Shann Ching, Karimi, Hassan A., ...
An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards...
Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES
Chennubhotla, Chakra, Bahar, Ivet
We introduce a novel approach for elucidating the potential pathways of allosteric communication in biomolecular systems. The methodology, based on Markov propagation of ‘information' across the...
Common Mechanism of Pore Opening Shared by Five Different Potassium Channels
Shrivastava, Indira H., Bahar, Ivet
A fundamental question associated with the function of ion channels is the conformational changes that allow for reversibly opening/occluding the pore through which the cations permeate. The recently...
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
Chennubhotla, Chakra, Bahar, Ivet
Elastic network (EN) models have been widely used in recent years for describing protein dynamics, based on the premise that the motions naturally accessible to native structures are relevant to...
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model
Ozkan, S. Banu, Dill, Ken A., Bahar, Ivet
Do two-state proteins fold by pathways or funnels? Native-state hydrogen exchange experiments show discrete nonnative structures in equilibrium with the native state. These could be called hidden...
Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis
Bagci, Elife Z., Vodovotz, Yoram, Billiar, Timothy R., Ermentrout, Bard, Bahar, Ivet
Despite the establishment of the important role of nitric oxide (NO) on apoptosis, a molecular- level understanding of the origin of its dichotomous pro- and anti-apoptotic effects has been elusive....
Analysis of correlated mutations in HIV-1 protease using spectral clustering
Liu, Ying, Eyal, Eran, Bahar, Ivet
Motivation: The ability of human immunodeficiency virus-1 (HIV-1) protease to develop mutations that confer multi-drug resistance (MDR) has been a major obstacle in designing rational therapies...
Shrivastava, Indira H., Jiang, Jie, Amara, Susan G., Bahar, Ivet
Glutamate transporters, also referred to as excitatory amino acid transporters (EAATs), are membrane proteins that regulate glutamatergic signal transmission by clearing excess glutamate after its...
Yang, Zheng, Májek, Peter, Bahar, Ivet
Identification of pathways involved in the structural transitions of biomolecular systems is often complicated by the transient nature of the conformations visited across energy barriers and the...
With recent advances in single-molecule manipulation techniques, it is now possible to measure the mechanical resistance of proteins to external pulling forces applied at specific positions....
Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter
Gu, Yan, Shrivastava, Indira H., Amara, Susan G., Bahar, Ivet
Glutamate transporters are membrane proteins found in neurons and glial cells, which play a critical role in regulating cell signaling by clearing glutamate released from synapses. Although extensive...
Isin, Basak, Schulten, Klaus, Tajkhorshid, Emad, Bahar, Ivet
As one of the best studied members of the pharmaceutically relevant family of G-protein-coupled receptors, rhodopsin serves as a prototype for understanding the mechanism of G-protein-coupled...
The conformational flexibility of target proteins continues to be a major challenge in accurate modeling of protein–inhibitor interactions. A fundamental issue, yet to be clarified, is whether the...
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models
Lezon, Timothy R., Sali, Andrej, Bahar, Ivet
The nuclear pore complex (NPC) is the gate to the nucleus. Recent determination of the configuration of proteins in the yeast NPC at ∼5 nm resolution permits us to study the NPC global dynamics...
Bakan, Ahmet, Lazo, John S, Wipf, Peter, Brummond, Kay M, Bahar, Ivet
Dual-specificity phosphatases (DSPs) are important, but poorly understood, cell signaling enzymes that remove phosphate groups from tyrosine and serine/threonine residues on their substrate....