The energy landscape of the ribosome.

The ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is governed by an underlying energy landscape, there has been great interest to understand and quantify ribosome energetics. In the present review, we will focus on theoretical and computational strategies for probing the interactions that shape the energy landscape of the ribosome, with an emphasis on more recent studies of the elongation cycle. These efforts include the application of quantum mechanical methods for describing chemical kinetics, as well as classical descriptions to characterize slower (microsecond to millisecond) large-scale (10-100 Å) rearrangements, where motion is described in terms of diffusion across an energy landscape. Together, these studies provide broad insights into the factors that control a diverse range of dynamical processes in this assembly.

Pectoralis Major in Salvage Total Laryngectomy after Irradiation: Morbidity, Mortality, Functional, and Oncological Results in a Referral Center in Egypt.

BACKGROUND: Nonsurgical organ preservation protocols have seen a large diffusion worldwide in the last decades. Their oncological and functional effectiveness in a real-world setting has been recently questioned because of the high morbidity of salvage procedures. The aim of this study is to review the outcomes of postirradiation salvage total laryngectomy (STL) and reconstruction with pectoralis major flap. METHODS: This retrospective observational study included 37 cases of STL in the period from January 2015 to December 2021. Data for each patient were extracted from the hospital information system and reviewed. RESULTS: The 3-year overall and disease-specific survival are, respectively, 28% and 51%. Only seven recurrences after salvage surgery were recorded and all of them died from the disease. The other 14 deaths derived from comorbidities, with diabetes being the most significant predictive parameter for overall survival. Also, lower postoperative albumin levels were associated with a higher risk of death. CONCLUSIONS: Overall survival after STL and reconstruction with PMMF is low but most deaths are due to comorbidities and not to cancer progression or recurrence.

Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications.

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA Val . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome.

Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.

Protein synthesis by the ribosome requires large-scale rearrangements of the 'small' subunit (SSU; ∼1 MDa), including inter- and intra-subunit rotational motions. However, with nearly 2000 structures of ribosomes and ribosomal subunits now publicly available, it is exceedingly difficult to design experiments based on analysis of all known rotation states. To overcome this, we developed an approach where the orientation of each SSU head and body is described in terms of three angular coordinates (rotation, tilt and tilt direction) and a single translation. By considering the entire RCSB PDB database, we describe 1208 fully-assembled ribosome complexes and 334 isolated small subunits, which span >50 species. This reveals aspects of subunit rearrangements that are universal, and others that are organism/domain-specific. For example, we show that tilt-like rearrangements of the SSU body (i.e. 'rolling') are pervasive in both prokaryotic and eukaryotic (cytosolic and mitochondrial) ribosomes. As another example, domain orientations associated with frameshifting in bacteria are similar to those found in eukaryotic ribosomes. Together, this study establishes a common foundation with which structural, simulation, single-molecule and biochemical efforts can more precisely interrogate the dynamics of this prototypical molecular machine.

Identifying Strategies to Experimentally Probe Multidimensional Dynamics in the Ribosome.

The ribosome is a complex biomolecular machine that utilizes large-scale conformational rearrangements to synthesize proteins. For example, during the elongation cycle, the "head" domain of the ribosomal small subunit (SSU) is known to undergo transient rotation events that allow for movement of tRNA molecules (i.e., translocation). While the head may exhibit rigid-body-like properties, the precise relationship between experimentally accessible probes and multidimensional rotations has yet to be established. To address this gap, we perform molecular dynamics simulations of the translocation step of the elongation cycle in the ribosome, where the SSU head spontaneously undergoes rotation and tilt-like motions. With this data set (1250 simulated events), we used statistical and information-theory-based measures to identify possible single-molecule probes that can isolate SSU head rotation and head tilting. This analysis provides a molecular interpretation for previous single-molecule measurements, while establishing a framework for the design of next-generation experiments that may precisely probe the mechanistic and kinetic aspects of the ribosome.

Impact of Exogenously Sprayed Antioxidants on Physio-Biochemical, Agronomic, and Quality Parameters of Potato in Salt-Affected Soil.

Salinity is one of the harsh environmental stresses that destructively impact potato growth and production, particularly in arid regions. Exogenously applied safe-efficient materials is a vital approach for ameliorating plant growth, productivity, and quality under salinity stress. This study aimed at investigating the impact of foliar spray using folic acid (FA), ascorbic acid (AA), and salicylic acid (SA) at different concentrations (100, 150, or 200 mg/L) on plant growth, physiochemical ingredients, antioxidant defense system, tuber yield, and quality of potato (Solanum tuberosum L cv. Spunta) grown in salt-affected soil (EC = 7.14 dS/m) during two growing seasons. The exogenously applied antioxidant materials (FA, AA, and SA) significantly enhanced growth attributes (plant height, shoot fresh and dry weight, and leaves area), photosynthetic pigments (chlorophyll a and b and carotenoids), gas exchange (net photosynthetic rate, Pn; transpiration rate, Tr; and stomatal conductance, gs), nutrient content (N, P, and K), K+/ Na+ ratio, nonenzymatic antioxidant compounds (proline and soluble sugar content), enzymatic antioxidants (catalase (CAT), peroxidase (POX), superoxide dismutase (SOD), and ascorbate peroxidase (APX)) tuber yield traits, and tuber quality (dry matter, protein, starch percentage, total carbohydrates, and sugars percentage) compared with untreated plants in both seasons. Otherwise, exogenous application significantly decreased Na+ and Cl- compared to the untreated control under salt stress conditions. Among the assessed treatments, the applied foliar of AA at a rate of 200 mg/L was more effective in promoting salt tolerance, which can be employed in reducing the losses caused by salinity stress in potato grown in salt-affected soils.

SMOG 2 and OpenSMOG: Extending the limits of structure-based models.

Applying simulations with structure-based Go¯-like models has proven to be an effective strategy for investigating the factors that control biomolecular dynamics. The common element of these models is that some (or all) of the intra/inter-molecular interactions are explicitly defined to stabilize an experimentally determined structure. To facilitate the development and application of this broad class of models, we previously released the SMOG 2 software package. This suite allows one to easily customize and distribute structure-based (i.e., SMOG) models for any type of polymer-ligand system. The force fields generated by SMOG 2 may then be used to perform simulations in highly optimized MD packages, such as Gromacs, NAMD, LAMMPS, and OpenMM. Here, we describe extensions to the software and demonstrate the capabilities of the most recent version (SMOG v2.4.2). Changes include new tools that aid user-defined customization of force fields, as well as an interface with the OpenMM simulation libraries (OpenSMOG v1.1.0). The OpenSMOG module allows for arbitrary user-defined contact potentials and non-bonded potentials to be employed in SMOG models, without source-code modifications. To illustrate the utility of these advances, we present applications to systems with millions of atoms, long polymers and explicit ions, as well as models that include non-structure-based (e.g., AMBER-based) energetic terms. Examples include large-scale rearrangements of the SARS-CoV-2 Spike protein, the HIV-1 capsid with explicit ions, and crystallographic lattices of ribosomes and proteins. In summary, SMOG 2 and OpenSMOG provide robust support for researchers who seek to develop and apply structure-based models to large and/or intricate biomolecular systems.

The energetics of subunit rotation in the ribosome.

Protein synthesis in the cell is controlled by an elaborate sequence of conformational rearrangements in the ribosome. The composition of a ribosome varies by species, though they typically contain ∼ 50-100 RNA and protein molecules. While advances in structural techniques have revolutionized our understanding of long-lived conformational states, a vast range of transiently visited configurations can not be directly observed. In these cases, computational/simulation methods can be used to understand the mechanical properties of the ribosome. Insights from these approaches can then help guide next-generation experimental measurements. In this short review, we discuss theoretical strategies that have been deployed to quantitatively describe the energetics of collective rearrangements in the ribosome. We focus on efforts to probe large-scale subunit rotation events, which involve the coordinated displacement of large numbers of atoms (tens of thousands). These investigations are revealing how the molecular structure of the ribosome encodes the mechanical properties that control large-scale dynamics.

Impact of Graft Steatosis on Postoperative Complications after Liver Transplantation.

Background Steatotic grafts are more susceptible to ischemia-reperfusion injury than are normal grafts. Therefore, using steatotic grafts for liver transplantation (LT) is associated with high primary dysfunction and decreased survival rates. The aim of this study is to evaluate the impact of graft steatosis on post LT outcomes. Methods A retrospective cohort analysis of 271 LT recipients from 2005 to 2016 was performed and patients were classified based on two types of steatosis, macrosteatosis (MaS), and microsteatosis (MiS). Each category was subdivided into three groups according to the degree of steatosis: no (< 5%), mild (≥5 to < 30%), and moderate (≥30 to ≤60%). The primary hospital stays and 6-month postoperative complications were analyzed by the Clavien-Dindo classification system. Additionally, patient and graft survivals were studied. Results Significant differences were observed in grade III MaS ( p -value = 0.019) and grade V MiS ( p -value = 0.020). A high trend of early graft dysfunction was found in the moderate MaS and MiS groups; however, they were not statistically significant ( p -value = 0.199 and 0.282, respectively). Interestingly, the acute cellular rejection (ACR) rate was found to be inversely proportional to the degree of steatosis in both categories but it did not reach a significant level ( p -value = 0.161 and 0.111, respectively). Conclusion Excellent post LT long-term outcomes using grafts with mild and moderate steatosis were determined. Further studies are needed to evaluate the newly proposed relationship between ACR and steatosis.

Adult intussusception. An overlooked diagnosis in the emergency department.

OBJECTIVE: To study the appropriate method of diagnosis and management in adult intussusception (AI) focusing on the clinical manifestations, diagnostic tools, and management of this rare disease. METHODS: This retrospective study reviewed and analyzed the demographic data, clinical features, diagnosis, management, and pathology reports of all adult patients (18 years of age and older) with a diagnosis of intussusception admitted to Sohag University Hospital, Sohag, Egypt, and Najran Armed Forces Hospital, Najran, Kingdom of Saudi Arabia (KSA) from January 2004 to August 2012. RESULTS: From 2004-2012, 14 patients with AI were diagnosed and treated. Ages ranged from 22-63 years. Ten patients (71.4%) were males. Thirteen patients (92.9%) presented with abdominal pain. All patients were diagnosed after a CT scan, and confirmed at laparotomy. The lead point was found in all, except for 2 patients. Ileo-ileal and jejuno-jejunal intussusceptions represented most of our cases (64.3%), followed by ileocolic (28.5%), and colocolic (7.1%). The most common causes were Peutz-Jeghers polyps (5 cases), submucosal lipoma (2), and malignancy (2). Surgery was the treatment option in all except one patient. Postoperative complications occurred in 3 cases (21.4%). One patient died 28 days postoperatively due to septic shock and multiorgan failure. CONCLUSION: Owing to its rarity, AI needs a high index of suspicion especially in patients attending ERs with recurrent abdominal pain. A CT scan is of prime importance in the diagnosis, and surgical treatment is the preferred method of management.