Regulating highly dynamic unstructured proteins and their coding mRNAs (2009)
Abstract The lifetimes and conformations of intrinsically unstructured proteins (IUPs) and their mRNAs are orchestrated to ensure precision, speed and flexibility in biological control.
Xiang Li, Ozlem Keskin, Buyong Ma, Ruth Nussinov, Jie Liang, Human Genetics
*Corresponding authors
Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR (2007)
Zengjian Hu, Donnell Bowen, William M. Southerland, Antonio Del Sol, Yongping Pan, Ruth Nussinov, ...
Residue interaction networks and loop motions are important for catalysis in dihydrofolate reductase (DHFR). Here, we investigate the effects of ligand binding and chain connectivity on network...
Ma, Buyong, Pan, Yongping, Zheng, Jie, Levine, Arnold J., Nussinov, Ruth
The p53 tetramer recognizes specifically a 20-bp DNA element. Here, we examined symmetries encoded in p53 response elements (p53REs). We analyzed base inversion correlations within the half-site, as...
Ligand Binding and Circular Permutation modify Residue Interaction Network in DHFR (2007)
Zengjian Hu, Donnell Bowen, William M Southerland, Antonio Del Sol, Yongping Pan, Ruth Nussinov, ...
Residue interaction networks and loop motions are important for catalysis in dihydrofolate reductase (DHFR). Here we investigate the effects of ligand binding and chain connectivity on network...
Jang, Hyunbum, Ma, Buyong, Nussinov, Ruth
Abstract Background Protegrin-1 (PG-1) is known as a potent antibiotic peptide; it prevents infection via an attack on the membrane surface of invading microorganisms. In the membrane, the peptide...
BMC Structural Biology BioMed Central (2007)
Hyunbum Jang, Buyong Ma, Ruth Nussinov, Open Access
Research article Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect
Symmetries in the p53 response-element (p53RE) encode binding modes for p53 tetramer to recognize DNA. We investigated the molecular mechanisms and biological implications of the possible binding...
In silico protein design by combinatorial assembly of protein building blocks (2004)
Tsai, Hui-Hsu (Gavin), Tsai, Chung-Jung, Ma, Buyong, Nussinov, Ruth
Utilizing concepts of protein building blocks, we propose a de novo computational algorithm that is similar to combinatorial shuffling experiments. Our goal is to engineer new naturally occurring...
Access the most recent version at doi: 10.1110/ps.0306103 References (2003)
Buyong Ma, Ruth Nussinov, Email Alerting, Buyong Ma, Ruth Nussinov
service
Li, Wen, Ma, Buyong, Shapiro, Bruce A.
The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the binding...
We have investigated free energy landscape [MM/PBSA + normal modes entropy] of permutations in the G peptide (41–56) from the protein G B1 domain by studying six isomers corresponding to moving the...
Molecular dynamics simulations of the unfolding of {beta}2-microglobulin and its variants (2003)
In this study, we examined the unfolding processes of native β2‐microglobulin and two related variants, one with an N‐terminal hexapeptide deletion ΔN6 and another with Lys57–Asp58...
The aggregation observed in protein conformational diseases is the outcome of significant new β-sheet structure not present in the native state. Peptide model systems have been useful in studies of...
Ma, Buyong, Shatsky, Maxim, Wolfson, Haim J., Nussinov, Ruth
Here, we comment on the steadily increasing body of data showing that proteins with specificity actually bind ligands of diverse shapes, sizes, and composition. Such a phenomenon is not surprising...
Access the most recent version at doi: 10.1110/ps.21302 References (2001)
Buyong Ma, Maxim Shatsky, Haim J. Wolfson, Ruth Nussinov, Email Alerting
Multiple diverse ligands binding at a single protein site: A matter of
Sham, Yuk Yin, Ma, Buyong, Tsai, Chung-Jung, Nussinov, Ruth
We have carried out molecular dynamics simulations of the native dihydrofolate reductase from Escherichia coli and several of its folded protein fragments at standard temperature. The simulations...
Binding and folding: in search of intramolecular chaperone-like building block fragments (2000)
Ma, Buyong, Tsai, Chung-Jung, Nussinov, Ruth
We propose an intramolecular chaperone which catalyzes folding and neither dissociates nor is cleaved. This uncleaved foldase is an intramolecular chain-linked chaperone, which constitutes a critical...
Folding funnels and binding mechanisms (1999)
Ma, Buyong, Kumar, Sandeep, Tsai, Chung-Jung, Nussinov, Ruth
The long-held views on lock-and-key versus induced fit in binding arose from the notion that a protein exists in a single, most stable conformation, dictated by its sequence. However, in solution...
We have mostly followed our initial plan described in the Statement of Work to investigate membrane disrupting peptide dynamics and membrane interactions. In the first year of research, we have...
Previously, we have studied the minimal oligomer size of an aggregate amyloid seed and the mechanism of seed growth with a multilayer β-sheet model. Under high temperature simulation conditions, our...
Li, Wen, Ma, Buyong, Shapiro, Bruce A.
The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the binding...
Ma, Buyong, Elkayam, Tal, Wolfson, Haim, Nussinov, Ruth
Polar residue hot spots have been observed at protein–protein binding sites. Here we show that hot spots occur predominantly at the interfaces of macromolecular complexes, distinguishing binding...
Ma, Buyong, Pan, Yongping, Gunasekaran, K., Venkataraghavan, R. Babu, Levine, Arnold J., Nussinov, Ruth
p53, the tumor suppressor protein, functions as a dimer of dimers. However, how the tetramer binds to the DNA is still an open question. In the crystal structure, three copies of the p53 monomers...
Zanuy, David, Ma, Buyong, Nussinov, Ruth
Experimentally, short peptides have been shown to form amyloids similar to those of their parent proteins. Consequently, they present useful systems for studies of amyloid conformation. Here we...
The Stability and Dynamics of the Human Calcitonin Amyloid Peptide DFNKF
Tsai, Hui-Hsu (Gavin), Zanuy, David, Haspel, Nurit, Gunasekaran, Kannan, Ma, Buyong, Tsai, Chung-Jung, ...
The stability and dynamics of the human calcitonin-derived peptide DFNKF (hCT15–19) are studied using molecular dynamics (MD) simulations. Experimentally, this peptide is highly amyloidogenic and...
Haliloglu, Turkan, Keskin, Ozlem, Ma, Buyong, Nussinov, Ruth
The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and...
Previously, we have studied the minimal oligomer size of an aggregate amyloid seed and the mechanism of seed growth with a multilayer β-sheet model. Under high temperature simulation conditions, our...
Li, Wen, Ma, Buyong, Shapiro, Bruce A.
The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the binding...
Ma, Buyong, Elkayam, Tal, Wolfson, Haim, Nussinov, Ruth
Polar residue hot spots have been observed at protein–protein binding sites. Here we show that hot spots occur predominantly at the interfaces of macromolecular complexes, distinguishing binding...
Ma, Buyong, Pan, Yongping, Gunasekaran, K., Venkataraghavan, R. Babu, Levine, Arnold J., Nussinov, Ruth
p53, the tumor suppressor protein, functions as a dimer of dimers. However, how the tetramer binds to the DNA is still an open question. In the crystal structure, three copies of the p53 monomers...
Zanuy, David, Ma, Buyong, Nussinov, Ruth
Experimentally, short peptides have been shown to form amyloids similar to those of their parent proteins. Consequently, they present useful systems for studies of amyloid conformation. Here we...
The Stability and Dynamics of the Human Calcitonin Amyloid Peptide DFNKF
Tsai, Hui-Hsu (Gavin), Zanuy, David, Haspel, Nurit, Gunasekaran, Kannan, Ma, Buyong, Tsai, Chung-Jung, ...
The stability and dynamics of the human calcitonin-derived peptide DFNKF (hCT15–19) are studied using molecular dynamics (MD) simulations. Experimentally, this peptide is highly amyloidogenic and...
Haliloglu, Turkan, Keskin, Ozlem, Ma, Buyong, Nussinov, Ruth
The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and...
Ma, Buyong, Pan, Yongping, Zheng, Jie, Levine, Arnold J., Nussinov, Ruth
The p53 tetramer recognizes specifically a 20-bp DNA element. Here, we examined symmetries encoded in p53 response elements (p53REs). We analyzed base inversion correlations within the half-site, as...
Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR
Hu, Zengjian, Bowen, Donnell, Southerland, William M, Del Sol, Antonio, Pan, Yongping, Nussinov, Ruth, ...
Residue interaction networks and loop motions are important for catalysis in dihydrofolate reductase (DHFR). Here, we investigate the effects of ligand binding and chain connectivity on network...
Structural Stability and Dynamics of an Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35
Zheng, Jie, Ma, Buyong, Tsai, Chung-Jung, Nussinov, Ruth
A seven amino acid yeast prion sup-35 fragment (GNNQQNY) forms amyloid fibrils. The availability of its detailed atomic oligomeric structure makes it a good model for studying the early stage of...
Interaction of Protegrin-1 with Lipid Bilayers: Membrane Thinning Effect
Jang, Hyunbum, Ma, Buyong, Woolf, Thomas B., Nussinov, Ruth
Protegrins (PG) are important in defending host tissues, preventing infection via an attack on the membrane surface of invading microorganisms. Protegrins have powerful antibiotic abilities, but the...
Symmetries in the p53 response-element (p53RE) encode binding modes for p53 tetramer to recognize DNA. We investigated the molecular mechanisms and biological implications of the possible binding...
In silico protein design by combinatorial assembly of protein building blocks
Tsai, Hui-Hsu (Gavin), Tsai, Chung-Jung, Ma, Buyong, Nussinov, Ruth
Utilizing concepts of protein building blocks, we propose a de novo computational algorithm that is similar to combinatorial shuffling experiments. Our goal is to engineer new naturally occurring...
Energy landscape and dynamics of the β-hairpin G peptide and its isomers: Topology and sequences
We have investigated free energy landscape [MM/PBSA + normal modes entropy] of permutations in the G peptide (41–56) from the protein G B1 domain by studying six isomers corresponding to moving the...
Sham, Yuk Yin, Ma, Buyong, Tsai, Chung-Jung, Nussinov, Ruth
We have carried out molecular dynamics simulations of the native dihydrofolate reductase from Escherichia coli and several of its folded protein fragments at standard temperature. The simulations...
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
Ma, Buyong, Shatsky, Maxim, Wolfson, Haim J., Nussinov, Ruth
Here, we comment on the steadily increasing body of data showing that proteins with specificity actually bind ligands of diverse shapes, sizes, and composition. Such a phenomenon is not surprising...
Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation
The aggregation observed in protein conformational diseases is the outcome of significant new β-sheet structure not present in the native state. Peptide model systems have been useful in studies of...
Zheng, Jie, Jang, Hyunbum, Ma, Buyong, Tsai, Chung-Jun, Nussinov, Ruth
We investigate Aβ17-42 protofibril structures in solution using molecular dynamics simulations. Recently, NMR and computations modeled the Aβ protofibril as a longitudinal stack of U-shaped...
Regulating highly dynamic unstructured proteins and their coding mRNAs
Orchestration of the lifetimes and conformations of intrinsically unstructured proteins and their mRNAs ensure precision and flexibility in biological control.
Jang, Hyunbum, Ma, Buyong, Lal, Ratnesh, Nussinov, Ruth
Antimicrobial peptides (AMPs) induce cytotoxicity by altering membrane permeability. The electrical properties of membrane-associated AMPs as well as their cellular effects have been extensively...