Functional aspects of protein flexibility

Teilum, Kaare; Olsen, Johan G.; Kragelund, Birthe B.

doi:10.1007/s00018-009-0014-6

Cited by 208 publications

(164 citation statements)

References 168 publications

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“…This increase in vibrational entropy might explain, at least in part, the increased entropy gain associated with adenophostin A binding. The larger T⌬S for adenophostin A relative to IP 3 binding would also be consistent with the larger apolar surface of adenophostin A, causing a greater entropy gain from ligand desolvation and hydrophobic interactions during binding (Teilum et al, 2009).…”

Section: Discussionmentioning

confidence: 68%

Binding of Inositol 1,4,5-trisphosphate (IP₃) and Adenophostin A to the N-Terminal region of the IP₃Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP₃Receptor Ligand

Zhao¹,

Rossi²,

Riley³

et al. 2010

Mol Pharmacol

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Inositol 1,4,5-trisphosphate (IP 3 ) receptors (IP 3 R) are intracellular Ca 2ϩ channels. Their opening is initiated by binding of IP 3 to the IP 3 -binding core (IBC; residues 224 -604 of IP 3 R1) and transmitted to the pore via the suppressor domain (SD; residues 1-223). The major conformational changes leading to IP 3 R activation occur within the N terminus (NT; residues 1-604). We therefore developed a high-throughput fluorescence polarization (FP) assay using a newly synthesized analog of IP 3 (Foskett et al., 2007). All IP 3 R are tetrameric and each subunit of approximately 2700 residues has an IP 3 -binding core (IBC; residues 224-604 of rat IP 3 R1) near its N terminus and six transmembrane domains toward the C terminus (Fig. 1A). The last pair of transmembrane domains with their intervening luminal loops from the four subunits form the pore. All three subtypes of vertebrate IP 3 R and the single subtype in invertebrates share a similar structural organization. It remains unclear how IP 3 binding to the IBC opens the pore, but the Nterminal suppressor domain (SD; residues 1-223) is involved. Removal of the SD uncouples IP 3 binding from gating (Uchida et al., 2003), a region within the N terminus that includes the SD interacts directly with residues close to the pore (Boehning and Joseph, 2000), and conformational changes initiated by IP 3 pass to the pore entirely via the SD ). These observations are presently supported by only limited knowledge of the structure of IP 3 R. There are high-resolution structures of the SD (Bosanac et al., 2005) and of the IBC with IP 3 bound (Bosanac et al., 2002), and there are several, somewhat inconsistent low-resolution (ϳ30 Å) structures of the entire IP 3 R (Taylor et al., 2004).

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Section: Discussionmentioning

confidence: 68%

Binding of Inositol 1,4,5-trisphosphate (IP₃) and Adenophostin A to the N-Terminal region of the IP₃Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP₃Receptor Ligand

Zhao¹,

Rossi²,

Riley³

et al. 2010

Mol Pharmacol

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“…Nuclear magnetic resonance (NMR) spectroscopy is the key technique to study dynamics and conformational states of proteins in solution at atomic resolution 10,11 . NMR-based case studies [12][13][14] have indicated that the level of conformational exchange of amino-acid residues is directly related to their dynamics, with fast dynamics indicating fast interchange between many (different) conformations.…”

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confidence: 99%

From protein sequence to dynamics and disorder with DynaMine

et al. 2013

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Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine-a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.

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“…Proteins possess many biological functions including binding, catalysis, operating as molecular switches, and serving as structural components of cells and organisms [1,2] and play an important role in the transportation and deposition of various endogenous and exogenous substances [3,4]. In recent years, the interaction of protein with small molecules has become a hot spot in the fields of chemistry, biology, and medicine [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Determination of the Binding Parameters between Proteins and Luminol by Chemiluminescence Using Flow Injection Technique

Guo

Chen

Song

2013

ISRN Analytical Chemistry

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The interaction behavior of bovine serum albumin (BSA), lysozyme (LYS), myoglobin (MB), and catalase (CAT) with luminol, respectively, was first studied by chemiluminescence (CL) using flow injection (FI) technique based on the fact that the studied proteins can enhance the CL intensity of luminol. A FI-CL model of protein-luminol interaction, lg[( 0 − )/ ] = 1/ lg[ ]+1/ lg + 2lg , was constructed, and the interaction parameters of BSA, LYS, MB, and CAT with luminol were determined accordingly. The binding constants are in the descending order of CAT > MB > LYS > BSA at the level of 10 5 to 10 7 L mol −1 , and the number of binding sites of luminol to BSA or LYS is around 2 and to MB or CAT is around 1. The results of thermodynamic parameters (Δ , Δ , and Δ ) showed that the binding processes of luminol to the four proteins are spontaneous mainly through the hydrophobic force.

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Functional aspects of protein flexibility

Cited by 208 publications

References 168 publications

Binding of Inositol 1,4,5-trisphosphate (IP₃) and Adenophostin A to the N-Terminal region of the IP₃Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP₃Receptor Ligand

Binding of Inositol 1,4,5-trisphosphate (IP₃) and Adenophostin A to the N-Terminal region of the IP₃Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP₃Receptor Ligand

From protein sequence to dynamics and disorder with DynaMine

Determination of the Binding Parameters between Proteins and Luminol by Chemiluminescence Using Flow Injection Technique

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Functional aspects of protein flexibility

Cited by 208 publications

References 168 publications

Binding of Inositol 1,4,5-trisphosphate (IP3) and Adenophostin A to the N-Terminal region of the IP3Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP3Receptor Ligand

Binding of Inositol 1,4,5-trisphosphate (IP3) and Adenophostin A to the N-Terminal region of the IP3Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP3Receptor Ligand

From protein sequence to dynamics and disorder with DynaMine

Determination of the Binding Parameters between Proteins and Luminol by Chemiluminescence Using Flow Injection Technique

Contact Info

Product

Resources

About

Binding of Inositol 1,4,5-trisphosphate (IP₃) and Adenophostin A to the N-Terminal region of the IP₃Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP₃Receptor Ligand

Binding of Inositol 1,4,5-trisphosphate (IP₃) and Adenophostin A to the N-Terminal region of the IP₃Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP₃Receptor Ligand