Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States

Nguyen, Dan; Hoffpauir, Zoe A.; Iwahara, Junji

doi:10.1021/acs.biochem.7b00885

Cited by 20 publications

(29 citation statements)

References 28 publications

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“…One underlying theme to all of the mechanisms reported above is the conformational malleability of DBDs. The co-evolved but frustrated landscape of DBDs can thus manifest as complex binding thermodynamics ( 37–40 ), anomalous heat capacity profiles ( 41 ), downhill-like folding mechanistic behaviors ( 14 ) and large dynamics even in the DNA-bound form ( 42 , 43 ). An extreme case is that of a DBD folding upon binding to DNA (or vice versa), while it remains disordered in the absence of DNA.…”

Section: Introductionmentioning

confidence: 99%

Tunable order–disorder continuum in protein–DNA interactions

Munshi

Gopi

Asampille

et al. 2018

Nucleic Acids Research

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DNA-binding protein domains (DBDs) sample diverse conformations in equilibrium facilitating the search and recognition of specific sites on DNA over millions of energetically degenerate competing sites. We hypothesize that DBDs have co-evolved to sense and exploit the strong electric potential from the array of negatively charged phosphate groups on DNA. We test our hypothesis by employing the intrinsically disordered DBD of cytidine repressor (CytR) as a model system. CytR displays a graded increase in structure, stability and folding rate on increasing the osmolarity of the solution that mimics the non-specific screening by DNA phosphates. Electrostatic calculations and an Ising-like statistical mechanical model predict that CytR exhibits features of an electric potential sensor modulating its dimensions and landscape in a unique distance-dependent manner, while DNA plays the role of a non-specific macromolecular chaperone. Accordingly, CytR binds its natural half-site faster than the diffusion-controlled limit and even random DNA conforming to an electrostatic-steering binding mechanism. Our work unravels for the first time the synergistic features of a natural electrostatic potential sensor, a novel binding mechanism driven by electrostatic frustration and disorder, and the role of DNA in promoting distance-dependent protein structural transitions critical for switching between specific and non-specific DNA-binding modes.

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Section: Introductionmentioning

confidence: 99%

Tunable order–disorder continuum in protein–DNA interactions

Munshi

Gopi

Asampille

et al. 2018

Nucleic Acids Research

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“…In the crystal structure of the same complex, there are 9 ion pairs of phosphates and basic side chains with an interionic O···N distance being <6 Å. Additionally, one of the three basic side chains in the disordered tail, which is not resolved in the crystal structure, is known to interact with DNA. 59 Thus, the diffusion-based method can accurately determine the number of cations released upon protein–nucleic acid association. This method will be useful particularly for systems involving disordered interfaces that electrostatically interact with DNA or RNA.…”

Section: Counterion Release Upon Protein–nucleic Acid Associationmentioning

confidence: 99%

“…Solution NMR studies of Arg and Lys side chains at the protein–DNA/RNA interfaces showed that basic side chains interacting with phosphate groups are generally more mobile than basic side chains interacting with nucleotide bases. 12 , 59 , 64 − 68 This difference in mobility may be related to steric restriction and other interactions in the grooves compared with those with the phosphate. More importantly, however, the dynamic equilibria between the CIP state and the solvent-separated ion pair (SIP) enhance the mobility of basic side chains forming ion pairs with phosphates ( Figure 4 A).…”

Section: Dynamics Of Macromolecular Ion Pairsmentioning

confidence: 99%

Dynamics of Ionic Interactions at Protein–Nucleic Acid Interfaces

Pettitt

Iwahara

2020

Acc. Chem. Res.

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Conspectus Molecular association of proteins with nucleic acids is required for many biological processes essential to life. Electrostatic interactions via ion pairs (salt bridges) of nucleic acid phosphates and protein side chains are crucial for proteins to bind to DNA or RNA. Counterions around the macromolecules are also key constituents for the thermodynamics of protein–nucleic acid association. Until recently, there had been only a limited amount of experiment-based information about how ions and ionic moieties behave in biological macromolecular processes. In the past decade, there has been significant progress in quantitative experimental research on ionic interactions with nucleic acids and their complexes with proteins. The highly negatively charged surfaces of DNA and RNA electrostatically attract and condense cations, creating a zone called the ion atmosphere. Recent experimental studies were able to examine and validate theoretical models on ions and their mobility and interactions with macromolecules. The ionic interactions are highly dynamic. The counterions rapidly diffuse within the ion atmosphere. Some of the ions are released from the ion atmosphere when proteins bind to nucleic acids, balancing the charge via intermolecular ion pairs of positively charged side chains and negatively charged backbone phosphates. Previously, the release of counterions had been implicated indirectly by the salt-concentration dependence of the association constant. Recently, direct detection of counterion release by NMR spectroscopy has become possible and enabled more accurate and quantitative analysis of the counterion release and its entropic impact on the thermodynamics of protein–nucleic acid association. Recent studies also revealed the dynamic nature of ion pairs of protein side chains and nucleic acid phosphates. These ion pairs undergo transitions between two major states. In one of the major states, the cation and the anion are in direct contact and form hydrogen bonds. In the other major state, the cation and the anion are separated by water. Transitions between these states rapidly occur on a picosecond to nanosecond time scale. When proteins interact with nucleic acids, interfacial arginine (Arg) and lysine (Lys) side chains exhibit considerably different behaviors. Arg side chains show a higher propensity to form rigid contacts with nucleotide bases, whereas Lys side chains tend to be more mobile at the molecular interfaces. The dynamic ionic interactions may facilitate adaptive molecular recognition and play both thermodynamic and kinetic roles in protein–nucleic acid interactions.

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“…In particular, Iwahara and co-workers have shown that the heteronuclear in-phase single quantum coherence experiment (HISQC) is more sensitive at detecting side chain amine signals because of its ability to reduce the relaxation effect of hydrogen exchange on 15 N atoms [ 54 ]. The Iwahara group also developed much of the theory behind the relaxation of 15 N atoms in -NH 3 + groups and showed that DNA binding to a protein changes dynamics of some of its lysine and arginine residues [ 55 , 56 ]. Their methodology is easily adaptable to GAG-binding proteins.…”

Section: Characterizing Lysine and Arginine Residues In Gag-bindinmentioning

confidence: 99%

“…Methods also exist to look at the relaxation of the 15 N atom in lysine side chain amine groups. They have been productively applied to the study of DNA-binding proteins [ 55 , 56 ]. Although there is currently no report of application of these methods to GAG-binding proteins, the utilization of these methods on GAG-binding proteins should shed important insights into protein-GAG interactions.…”

Section: Probing Gag-induced Changes In Protein Dynamics and Oligomentioning

confidence: 99%

Glycosaminoglycan-Protein Interactions by Nuclear Magnetic Resonance (NMR) Spectroscopy

Pomin

Wang

2018

Molecules

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Nuclear magnetic resonance (NMR) spectroscopy is one of the most utilized and informative analytical techniques for investigating glycosaminoglycan (GAG)-protein complexes. NMR methods that are commonly applied to GAG-protein systems include chemical shift perturbation, saturation transfer difference, and transferred nuclear Overhauser effect. Although these NMR methods have revealed valuable insight into the protein-GAG complexes, elucidating high-resolution structural and dynamic information of these often transient interactions remains challenging. In addition, preparation of structurally homogeneous and isotopically enriched GAG ligands for structural investigations continues to be laborious. As a result, understanding of the structure-activity relationship of GAGs is still primitive. To overcome these deficiencies, several innovative NMR techniques have been developed lately. Here, we review some of the commonly used techniques along with more novel methods such as waterLOGSY and experiments to examine structure and dynamic of lysine and arginine side chains to identify GAG-binding sites. We will also present the latest technology that is used to produce isotopically enriched as well as paramagnetically tagged GAG ligands. Recent results that were obtained from solid-state NMR of amyloid’s interaction with GAG are also presented together with a brief discussion on computer assisted modeling of GAG-protein complexes using sparse experimental data.

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Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States

Cited by 20 publications

References 28 publications

Tunable order–disorder continuum in protein–DNA interactions

Tunable order–disorder continuum in protein–DNA interactions

Dynamics of Ionic Interactions at Protein–Nucleic Acid Interfaces

Glycosaminoglycan-Protein Interactions by Nuclear Magnetic Resonance (NMR) Spectroscopy

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