Automated multiconformer model building for X-ray crystallography and cryo-EM.

In their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble averages, reflecting molecules in various conformations. Yet, most models derived from these maps explicitly represent only a single conformation, overlooking the complexity of biomolecular structures. To accurately reflect the diversity of biomolecular forms, there is a pressing need to shift toward modeling structural ensembles that mirror the experimental data. However, the challenge of distinguishing signal from noise complicates manual efforts to create these models. In response, we introduce the latest enhancements to qFit, an automated computational strategy designed to incorporate protein conformational heterogeneity into models built into density maps. These algorithmic improvements in qFit are substantiated by superior Rfree and geometry metrics across a wide range of proteins. Importantly, unlike more complex multicopy ensemble models, the multiconformer models produced by qFit can be manually modified in most major model building software (e.g., Coot) and fit can be further improved by refinement using standard pipelines (e.g., Phenix, Refmac, Buster). By reducing the barrier of creating multiconformer models, qFit can foster the development of new hypotheses about the relationship between macromolecular conformational dynamics and function.

No Difference in Complication Rates or Patient-Reported Outcomes Between Bone-Patella Tendon-Bone and Quadriceps Tendon Autograft for Anterior Cruciate Ligament Reconstruction.

Purpose: To compare subjective outcomes and complications of anterior cruciate ligament reconstruction (ACLR) using either bone-patellar tendon-bone (BPTB) or quadriceps tendon (QT) autograft. Methods: A retrospective analysis of prospectively collected data identified consecutive cohorts of patients undergoing ACLR with either BPTB or QT autograft. Patients with less than 12-month follow-up and those undergoing concomitant osteotomies, cartilage restoration, and/or other ligament reconstruction procedures were excluded. Pre- and postsurgical patient-reported outcomes including International Knee Documentation Committee, Knee Injury and Osteoarthritis Outcome Score, Patient-Reported Outcomes Measurement Information System (PROMIS), Single Assessment Numeric Evaluation, Tegner, and Marx were compared between groups. Complications requiring reoperation were recorded. Results: One hundred nineteen patients met inclusion criteria, including 39 QT autografts and 80 BPTB autografts. Demographic information was comparable between groups. Mean follow-up was comparable between groups (QT 22.4 ± 10.6 months vs BPTB 28.5 ± 18.5 months, P = .06). At minimum 12-month follow-up (range 12.0-100.8 months), patients in both groups demonstrated statistically significant improvements in International Knee Documentation Committee (QT 60.0%, P < .0001; BPTB 57.7%, P < .0001), all Knee Injury and Osteoarthritis Outcome Score domains, PROMIS Mobility T-Score (QT 27.2%, P = .0001; BPTB 23.2%, P < .0001), PROMIS Global Physical Health (QT 14.4%, P = .002; BPTB 13.4%, P = .001), PROMIS Physical Function (QT 29.6%, P < .0001; BPTB 37.1%, P < .0001), PROMIS Pain Interference (QT -16.5%, P < .0001; BPTB -20.8%, P < .0001), Single Assessment Numeric Evaluation, (QT 76.9%, P < .0001; BPTB 73.3%, P < .0001), Tegner (QT 92.9%, P = .0002; BPTB 101.4%, P < .0001), and Marx (QT -26.6%, P = .02; BPTB -32.0%, P = .0002) with no statistically significant differences between the 2 groups. Overall postoperative reoperation rate did not differ between groups (QT 12.8% vs BPTB 23.8%, P = .2). Revision ACL reconstruction rate did not differ between groups (QT 5.1% vs BPTB 7.5%, P = .6). Conclusions: Patients undergoing autograft ACLR with either BPTB or QT demonstrated significant subjective improvements in patient-reported outcomes from preoperative values and no statistically significant differences in outcomes between the groups. Complication and revision ACLR rates were similar between the 2 groups. Level of Evidence: III, retrospective cohort study.

Ligand binding remodels protein side-chain conformational heterogeneity.

While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but it can provide information on both the anharmonic and harmonic contributions to conformational heterogeneity. Here, through multiconformer modeling of time- and space-averaged electron density, we measure conformational heterogeneity of 743 stringently matched pairs of crystallographic datasets that reflect unbound/apo and ligand-bound/holo states. When comparing the conformational heterogeneity of side chains, we observe that when binding site residues become more rigid upon ligand binding, distant residues tend to become more flexible, especially in non-solvent-exposed regions. Among ligand properties, we observe increased protein flexibility as the number of hydrogen bonds decreases and relative hydrophobicity increases. Across a series of 13 inhibitor-bound structures of CDK2, we find that conformational heterogeneity is correlated with inhibitor features and identify how conformational changes propagate differences in conformational heterogeneity away from the binding site. Collectively, our findings agree with models emerging from nuclear magnetic resonance studies suggesting that residual side-chain entropy can modulate affinity and point to the need to integrate both static conformational changes and conformational heterogeneity in models of ligand binding.

Proteins are the workhorses of our cells. They are large molecules that 'fold' into specific, often highly complex, three-dimensional configurations. These structures are not static, but rather dynamic and flexible. In other words, proteins can shift between different three-dimensional shapes to perform their tasks within the cell. To perform their roles, many proteins have to bind to small molecule ligands. Many ligands are drugs, which means that their effectiveness depends on their ability to bind to and impact the proteins involved in the disease they are treating. When a ligand binds to a protein, it can reshape the protein. For example, certain conformations of the protein, which were difficult for the protein to be in on its own, may become more stable when the ligand binds. Additionally, upon ligand binding, some parts of the protein may move relative to each other. Previous studies have shown that these movements can affect the interaction between ligand and protein. However, these studies only examined a small number of proteins. Therefore, Wankowicz et al. set out to determine, in greater detail, what happens to protein flexibility upon ligand binding. First, a pipeline was created to model alternative configurations of the protein both with and without ligands attached. These models measured flexibility within protein structures. The models revealed that when ligands bind to proteins, the flexibility of different regions of the protein changes ­ and does so in a consistent way. Proteins that become more rigid in the region interacting with their ligands become less rigid in other, distant regions, and vice versa. In other words, the rest of the protein is able to compensate for any changes in flexibility caused by ligand binding, which may contribute to how well a ligand binds to a protein. This study demonstrates the ability of ligands to affect the entire structure of the proteins they bind to, and therefore sheds new light on the role of proteins' innate conformational flexibility during this process. These results will contribute to our understanding of how the ligands and proteins involved in different cellular processes interact with each other ­ and, potentially, how these interactions can be manipulated.

qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps.

New X-ray crystallography and cryo-electron microscopy (cryo-EM) approaches yield vast amounts of structural data from dynamic proteins and their complexes. Modeling the full conformational ensemble can provide important biological insights, but identifying and modeling an internally consistent set of alternate conformations remains a formidable challenge. qFit efficiently automates this process by generating a parsimonious multiconformer model. We refactored qFit from a distributed application into software that runs efficiently on a small server, desktop, or laptop. We describe the new qFit 3 software and provide some examples. qFit 3 is open-source under the MIT license, and is available at https://github.com/ExcitedStates/qfit-3.0.

Intraflagellar transport velocity is governed by the number of active KIF17 and KIF3AB motors and their motility properties under load.

Homodimeric KIF17 and heterotrimeric KIF3AB are processive, kinesin-2 family motors that act jointly to carry out anterograde intraflagellar transport (IFT), ferrying cargo along microtubules (MTs) toward the tips of cilia. How IFT trains attain speeds that exceed the unloaded rate of the slower, KIF3AB motor remains unknown. By characterizing the motility properties of kinesin-2 motors as a function of load we find that the increase in KIF3AB velocity, elicited by forward loads from KIF17 motors, cannot alone account for the speed of IFT trains in vivo. Instead, higher IFT velocities arise from an increased likelihood that KIF3AB motors dissociate from the MT, resulting in transport by KIF17 motors alone, unencumbered by opposition from KIF3AB. The rate of transport is therefore set by an equilibrium between a faster state, where only KIF17 motors move the train, and a slower state, where at least one KIF3AB motor on the train remains active in transport. The more frequently the faster state is accessed, the higher the overall velocity of the IFT train. We conclude that IFT velocity is governed by (i) the absolute numbers of each motor type on a given train, (ii) how prone KIF3AB is to dissociation from MTs relative to KIF17, and (iii) how prone both motors are to dissociation relative to binding MTs.

Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer.

The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand binding was studied at the single-molecule level by combined force spectroscopy and Förster resonance energy transfer (smFRET), using an optical trap equipped for simultaneous smFRET. The 'Force-FRET' approach directly probes secondary and tertiary structural changes during folding, including events associated with binding. Concurrent transitions observed in smFRET signals and RNA extension revealed differences in helix-arm orientation between two previously-identified ligand-binding states that had been undetectable by spectroscopy alone. Our results show that the weaker binding state is able to bind to TPP, but is unable to form a tertiary docking interaction that completes the binding process. Long-range tertiary interactions stabilize global riboswitch structure and confer increased ligand specificity.

Observations of Dicke narrowing and speed dependence in air-broadened CO2 lineshapes near 2.06 µm.

Frequency-stabilized cavity ring-down spectroscopy was used to study CO2 lineshapes in the (20013) ← (00001) band centered near 2.06 µm. Two rovibrational transitions were chosen for this study to measure non-Voigt collisional effects for air-broadened lines over the pressure range of 7 kPa-28 kPa. Lineshape analysis for both lines revealed evidence of simultaneous Dicke (collisional) narrowing and speed-dependent effects that would introduce biases exceeding 2% in the retrieved air-broadening parameters if not incorporated in the modeling of CO2 lineshapes. Additionally, correlations between velocity- and phase/state changing collisions greatly reduced the observed Dicke narrowing effect. As a result, it was concluded that the most appropriate line profile for modeling CO2 lineshapes near 2.06 µm was the correlated speed-dependent Nelkin-Ghatak profile, which includes all of the physical effects mentioned above and leads to a consistent set of line shape parameters that are linear with gas pressure.

Traumatic carotid-rosenthal fistula treated with Jostent Graftmaster.

Traumatic injuries of the carotid artery may result in severe morbidity and mortality. The most common location of carotid artery injury is the cavernous segment, which may result in fistulous connection to the cavernous sinus and ophthalmic veins, which in turn lead to pressure symptoms in the ipsilateral orbit. Unlike the commonly reported direct traumatic carotid-cavernous fistula, we describe an unusual case of a 38-year-old man presented with a traumatic brain injury led to a fistula connection between the cavernous carotid artery and the ipsilateral basal vein of Rosenthal, with eventual drainage to the straight and transverse sinuses. The basal vein of Rosenthal is usually formed from confluence of anterior and middle cerebral veins deep in the Sylvian fissure and drain the insular cortex and the cerebral peduncles to the vein of Galen. Immediate endovascular deployment of a covered stent in the cavernous carotid artery allowed sealing the laceration site. Three months follow up showed a non-focal neurological examination and healed carotid laceration over the covered stent.