Conserved proline residues prevent dimerization and aggregation in the β-lactamase BlaC

Evolution leads to conservation of amino acid residues in protein families. Conserved proline residues are usually considered to ensure the correct folding and to stabilize the three-dimensional structure. Surprisingly, proline residues that are highly conserved in class A β-lactamases were found to tolerate various substitutions without large losses in enzyme activity. We investigated the roles of three conserved prolines at positions 107, 226, and 258 in the β-lactamase BlaC from Mycobacterium tuberculosis and found that mutations can lead to dimerization of the enzyme and an overall less stable protein that is prone to aggregate over time. For the variant Pro107Thr, the crystal structure shows dimer formation resembling domain swapping. It is concluded that the proline substitutions loosen the structure, enhancing multimerization. Even though the enzyme does not lose its properties without the conserved proline residues, the prolines ensure the long-term structural integrity of the enzyme.

[Consultations by senior physicians in general and abdominal surgery for other medical disciplines over 10 years at a tertiary center-Is a fast time-consuming processing necessary? : Spectrum of clinical findings, diagnoses and treatment decision making]

BACKGROUND

The challenges of an adequate, efficient and rational medical treatment and care of patients are always associated with an interprofessional activity of several specialist disciplines.

AIM

The spectrum of variable diagnoses and the profile of surgical decision-making with further surgical measures within the framework of senior physician consultation in general and visceral surgery for neighboring medical disciplines were analyzed on a representative patient cohort over a defined observational time period.

PATIENTS AND METHODS

All consecutive patients (n = 549 cases) were documented as part of a clinical systematic prospective single center observational study at a tertiary center using a computer-based patient registry over 10 years (1 October 2006-30 September 2016). The data were analyzed with respect to the spectrum of clinical findings, diagnoses, treatment decisions and the influencing factors as well as gender and age differences and time-dependent developmental trends using χ2-tests and U‑tests.

RESULTS (KEY POINTS)

The predominant discipline for requests for surgical consultation was cardiology (19.9%) followed by surgical disciplines (11.8%) and gastroenterology (11.3%). Disorders of wound healing (7.1%) and acute abdomen (7.1%) were predominant in the diagnostic profile. In 11.7% of the patients the indications for immediate surgery were derived, whereas in 12.9% elective surgery was recommended. The conformity rate of suspected and definitive diagnoses was only 58.4%.

CONCLUSION

The surgical consultation work is an important mainstay of a sufficient and especially timely clarification of surgically relevant questions in nearly all medical institutions and especially in a center. This serves i) the quality assurance of surgery in the clinical care of patients with need of additional interdisciplinary needs for surgical treatment in the daily practice of general and abdominal surgery in research on clinical care, ii) clinical marketing and monetary aspects in the sense of patient recruitment and iii) last but not least to provide emergency care of patients. Due to the high proportion of 12% of subsequent emergency operations, which were derived from requests for general and visceral surgical consultations, such requests must be processed promptly during working hours.

Robotic and laparoscopic liver resection-comparative experiences at a high-volume German academic center

Purpose

Minimally invasive liver surgery (MILS) is a feasible and safe procedure for benign and malignant tumors. There has been an ongoing debate on whether conventional laparoscopic liver resection (LLR) or robotic liver resection (RLR) is superior and if one approach should be favored over the other. We started using LLR in 2010, and introduced RLR in 2013. In the present paper, we report on our experiences with these two techniques as early adopters in Germany.

Methods

The data of patients who underwent MILS between 2010 and 2020 were collected prospectively in the Magdeburg Registry for Minimally Invasive Liver Surgery (MD-MILS). A retrospective analysis was performed regarding patient demographics, tumor characteristics, and perioperative parameters.

Results

We identified 155 patients fulfilling the inclusion criteria. Of these, 111 (71.6%) underwent LLR and 44 (29.4%) received RLR. After excluding cystic lesions, 113 cases were used for the analysis of perioperative parameters. Resected specimens were significantly bigger in the RLR vs. the LLR group (405 g vs. 169 g, p = 0.002); in addition, the tumor diameter was significantly larger in the RLR vs. the LLR group (5.6 cm vs. 3.7 cm, p = 0.001). Hence, the amount of major liver resections (three or more segments) was significantly higher in the RLR vs. the LLR group (39.0% vs. 16.7%, p = 0.005). The mean operative time was significantly longer in the RLR vs. the LLR group (331 min vs. 181 min, p = 0.0001). The postoperative hospital stay was significantly longer in the RLR vs. the LLR group (13.4 vs. LLR 8.7 days, p = 0.03). The R0 resection rate for solid tumors was higher in the RLR vs. the LLR group but without statistical significance (93.8% vs. 87.9%, p = 0.48). The postoperative morbidity ≥ Clavien-Dindo grade 3 was 5.6% in the LLR vs. 17.1% in the RLR group (p = 0.1). No patient died in the RLR but two patients (2.8%) died in the LLR group, 30 and 90 days after surgery (p = 0.53).

Conclusion

Minimally invasive liver surgery is safe and feasible. Robotic and laparoscopic liver surgery shows similar and adequate perioperative oncological results for selected patients. RLR might be advantageous for more advanced and technically challenging procedures.

Oncological outcome after hyperthermic isolated limb perfusion for primarily unresectable versus locally recurrent soft tissue sarcoma of extremities

INTRODUCTION

The management of locally advanced extremity soft tissue sarcomas, particularly in terms of a limb salvage strategy, represents a challenge, especially in recurrent tumors. In the context of a patient-tailored multimodal therapy, hyperthermic isolated limb perfusion (ILP) is a promising limb-saving treatment option. We report the outcome of patients with primarily irresectable and locally recurrent soft tissue sarcoma (STS) treated by ILP.

PATIENTS AND METHODS

Data about patient demographics, clinical und histopathological characteristics, tumor response, morbidity and oncological outcome of all patients with STS, who underwent an ILP at our institution in a 10-year period, were retrospectively detected and analyzed.

RESULTS

The cohort comprised 30 patients. Two patients were treated with ILP for palliative tumor control, 13 patients because of a local recurrent soft tissue sarcoma (rSTS) and 15 patients because of primarily unresectable soft tissue sarcoma (puSTS). 25 of the 28 patients with curative intention received surgery after ILP (11 pts with rSTS and 14 pts with puSTS). Histopathologically we observed complete response in 6 patients (24%) and partial responses in 19 patients (76%) with a significant better remission in patients with puSTS (p = 0,043). Limb salvage rate was 75%. Mean follow-up was 69 months [range 13-142 months]. Seven (7/11; 64%) patients with rSTS and one (1/14; 7%) patient with puSTS developed local recurrence after ILP and surgery, whereas eight (8/13; 62%) rSTS patients and seven (7/15; 47%) puSTS patients developed distant metastasis. During follow-up, eight patients (28.5%) died of disease (5/13; 38%) rSTS and 3/15 (20%) puSTS. ILP in the group of previously irradiated sarcoma patients (n = 13) resulted in a limb salvage rate of 69% and was not associated in an increased risk for adverse events.

DISCUSSION

ILP for advanced extremity STS is a treatment option for both puSTS and rSTS resulting in good local control and should be considered in multimodal management. ILP is also a good option for patients after radiation history.

A falciform ligament flap surface sealing technique for laparoscopic and robotic-assisted liver surgery

Whether sealing the hepatic resection surface after liver surgery decreases morbidity is still unclear. Nevertheless, various methods and materials are currently in use for this procedure. Here, we describe our experience with a simple technique using a mobilized falciform ligament flap in minimally invasive liver surgery (MILS). We retrospectively analyzed the charts from 46 patients who received minor MILS between 2011 and 2019 from the same surgical team in a university hospital setting in Germany. Twenty-four patients underwent laparoscopic liver resection, and 22 patients received robotic-assisted liver resection. Sixteen patients in the laparoscopic group and fourteen in the robotic group received a falciform ligament flap (FLF) to cover the resection surface after liver surgery. Our cohort was thus divided into two groups: laparoscopic and robotic patients with (MILS + FLF) and without an FLF (MILS-FLF). Twenty-eight patients (60.9%) in our cohort were male. The overall mean age was 56.8 years (SD 16.8). The mean operating time was 249 min in the MILS + FLF group vs. 235 min in the MILS-FLF group (p = 0.682). The mean blood loss was 301 ml in the MILS + FLF group vs. 318 ml in the MILS-FLF group (p = 0.859). Overall morbidity was 3.3% in the MILS + FLF group vs. 18.8% in the MILS-FLF group (p = 0.114). One patient in the MILS-FLF group (overall 2.2%), who underwent robotic liver surgery, developed bile leakage, but this did not occur in the MILS + FLF group. Covering the resection surface of the liver after minor minimally invasive liver resection with an FLF is a simple and cost-effective technique that does not prolong surgical time or negatively affect other perioperative parameters. In fact, it is a safe add-on step during MILS that may reduce postoperative morbidity. Further studies with larger cohorts will be needed to substantiate our proof of concept and results.

Mesothelial cyst of the round ligament

Mesothelial cyst of the round ligament is a rare finding in females, with only a few cases reported so far. A case of a 25 year old female patient presenting with a palpable mass in her right inguinal region is presented. The preoperative investigation through ultrasound (U/S), computed tomography (CT) and magnetic resonance imaging (MRI) revealed the presence of an intraabdominal cystic lobular mass in the inguinal canal, in contact with the femoral vessels. The mass was excised and the diagnosis of a benign mesothelial cyst was made through pathological examination. Even though it is a rare condition, it is advisable that clinicians consider in the differential diagnosis when evaluating a non-reducible mass in the inguinal region of a female patient.

[Robotic-Assisted Liver Surgery]

BACKGROUND

The advantages of minimally invasive liver resections for selected patients are evident. Robots provide new innovations that will influence minimally invasive liver surgery in the future. This article presents our initial experience with this technology in our patient population. Material und Methods: In 14 patients with benign or malignant liver tumours, robotic-assisted liver surgery was performed. Selection criteria were compensated liver function and resection of ≤ 3 liver segments. Chronic liver disease or previous abdominal surgery were no exclusion criteria.

RESULTS

Malignant liver tumours were removed in 10 patients (71%) and benign symptomatic liver tumors in 3 patients (21%), respectively, with histopathologically negative margins (R0). One patient suffering from HCC underwent intraoperative ablation. In one case (7%) conversion was necessary. Mean operation time was 296 min (120-458 min); mean estimated blood loss was 319 ± 298 ml. The mean hospital stay of the patients was 8 days (3-17 days). Three patients (21%) suffered from postoperative complications, which were manageable by conservative treatment (Clavien-Dindo I) in 2 cases (14%). One patient (7%) needed endoscopic treatment for postoperative bile leak (Clavien-Dindo III a). No patient died intra- or perioperatively.

CONCLUSION

Robotic-assisted liver surgery is a safe procedure, which provides patients with all benefits of minimally invasive surgery. This highly advanced technology requires surgeons to strive for an increasing level of specialisation, in addition to being well-trained in liver surgery. Hence, a clear definition of the procedures and standardised teaching programs are necessary.

Long-term outcome of liver transplantation as treatment modality in patients with hepatocellular carcinoma in cirrhosis: a single-center experience

BACKGROUND

Hepatocellular carcinoma (HCC) is among the most frequent malignant diseases worldwide. In the vast majority of cases, it is associated with liver cirrhosis. Liver transplantation (OLT) is potentially the gold standard treatment for patients suffering HCC in cirrhosis, because of synchronous eradication of HCC and of the underlying hepatic disease. The aim of this study was to evaluate long-term outcomes of OLT in HCC patients.

MATERIAL AND METHODS

Between January 2000 and December 2011, 43 patients who were diagnosed with HCC in liver cirrhosis and underwent OLT in our department, were identified from a prospective database. All patients received their grafts from deceased donors. We analyzed demographic data, laboratory values, number and size of lesions, primary liver disease, diagnostic methods, bridging therapy modalities, and postoperative outcomes, including complications, recurrences, and their treatment.

RESULTS

Patient follow-up as of January 2012 or to death ranged from 0 to 138 months (median, 59; mean, 63). None of the patients were lost to follow-up. The gender bias was 85%:15% (male:female) and the median age, 57.8 years (range, 44-69). The most common underlying diseases for cirrhosis and HCC were alcoholic (n = 12) and hepatitis C (n = 16). Thirty-one subjects underwent bridging therapy through transarterial chemoembolization (TACE), and/or radiofrequency ablation. All patients underwent OLT within the Milan criteria according to the preoperative evaluation and histopathologic examination of the explanted liver. Twenty-one of them suffered postoperative complications (48.8%). HCC recurrence, which occurred in 5 (10.4%), was treated by surgery (n = 3), systemic chemotherapy with sorafenib (n = 1), or TACE (n = 1).

CONCLUSIONS

OLT for HCC in cirrhosis, displays a relatively high complication rate. It shows good survivals with and low recurrence.

Is there a disadvantage to radical lymph node dissection in colon cancer?

BACKGROUND

The necessity for radical lymph node dissection for solid tumours was discussed in the past controversially. The aim of this study was to correlate the oncologic results of radical surgery for colon cancer with potential complications.

METHODS

A total of 1,453 patients with R0-resected colon cancer operated on between 1978 and 2004 were analysed in a prospective database. The follow-up was at least 5 years. Rates of survival, locoregional and distant recurrences and complications were calculated.

RESULTS

To compare the oncological outcome, the time frame was divided into five periods. In the last cohort (2000-2004), we observed in stage I-III tumours a 5-year cancer-related survival rate of 90.1 %, compared to 82.1 % in the first cohort (1978-1984) (p = 0.061). The local recurrence rate could be reduced from 6.5 to 3.2 % in the same cohorts (p = 0.059). It reached the level of significance in the multivariate analysis. The rates of distant metastases did not change. For patients with stage III, the 5-year cancer survival rates increased from 62.0 to 81.8 % (p = 0.005). Morbidity and mortality were comparable to other studies even to those with limited lymph node dissections.

CONCLUSION

Radical lymph node dissection in colon cancer is not associated with obvious disadvantages to the patient. Specific considerable side effects were not observed when the preparation is performed in embryonic planes preserving the autonomous nerves. The complication rates were not increased compared to other studies, even to those with limited lymphatic dissection. In addition, radical lymph node dissection in colon cancer may improve survival.

[Results of surgical treatment of hiatal hernia]

BACKGROUND

Hiatus hernias are considered as the most prominent form of diaphragmatic hernias. The passage is defined through the oesophageal hiatus, resulting in a superdiaphragmatic displacement of parts of the stomach or the complete stomach, respectively. In our work we investigated the treatment of partial thoracic stomach with both open and minimally invasive surgical procedures emphasising the view on operating data, the success of the surgery and recurrence rates. Patients with mesh insertion for hernia defect closures were considered separately.

MATERIAL AND METHOD

94 Patients were treated in the period from 01.01.2003 to 01.06.2010. The ratio male/female was 2 : 1. The median age was 66 years. All data were prospectively collected by means of surgical protocols and data from the central patient records and analysed retrospectively. The statistical analyses were performed with SPSS 18.0 (SPSS Inc., Chicago, IL, USA). Any existing significances were determined using the T-test.

RESULTS

Of the 94 patients, 65 were operated laparoscopically. In the case of nine patients an initial laparoscopic surgery had to be changed to an open procedure. The reasons for switching surgical procedures were splenic bleeding in the case of 2 patients, intestinal injury due to perforation by the trocar in one case and unclear surgical situs in 6 cases. The postoperative complication rate was 24 %. The main reasons were a delayed achievement of passage. The mortality rate was 0 %. The comparison between laparoscopic and open groups showed, by comparable complication and recurrence rates, a shorter recovery time in favour of patients operated on laparoscopically. Additionally it can be stated that a bridge closure with mesh (ePTFE) had no significant influence on the postoperative outcome. Therefore we cannot confirm the postulated poor postoperative results of other groups.

CONCLUSION

In summary, the clear trend in the surgical treatment of hiatus hernias is to minimally invasive surgery. Only for patients with multiple previous operations, who are expected to have strong adhesions, the operation with comparable morbidity and mortality rates can also be planned primarily as open. In this case, however, longer postoperative recovery times must be expected. Large defects can be treated with comparable complication and recurrence rates by mesh insertion (ePTFE).

The effect and safety of the treatment of recurrent hepatitis C infection after orthotopic liver transplantation with pegylated interferon α2b and ribavirin

INTRODUCTION

Recurrent hepatitis C infection in the posttransplant setting is a serious problem. The aim of this study was to evaluate the efficacy, safety, indications, optimal time of administration and adequate duration of antiviral therapy with pegylated interferon alpha 2 b (PEG-IFN) and ribavirin (RIB).

PATIENTS AND METHODS

Between 2003 and 2009, 16 patients received antiviral therapy (PEG-IFN: 0.8-1.6 μg/kg/wk, RIB 800-1200 mg/d) for at least 6 months. Patients with a biochemical without a virologicalresponse after 12 months of therapy received antiviral treatment for a further 6 months. Hepatitis C virus load was determined at 1, 3, 6, and 12 months after start of therapy. Liver biopsy was performed in all patients before the beginning and after the end of treatment.

RESULTS

The mean period of antiviral therapy was 14 months. The four patients who received the full-length treatment (12 months, 33%) showed sustained virological responses (SVR) and 8 showed virological and biochemical responses (VR, BR). Patients with SVR showed significant improvement in the grading and staging of HAI (histological activity index; P=.03). Nine patients had several side effects under antiviral treatment. Acute rejection episodes were not observed.

CONCLUSION

The antiviral treatment combination using PEG-IFN and RIB for recurrent hepatitis C is effective procedure. The SVR of 33% after 12 months of treatment with significant improvement in HAI grading and staging and stable HAI in all treated patients favor early initiation and 12-month administration of antiviral treatment. Furthermore, all patients with BR without VR, who underwent antiviral treatment for a further 6 months, achieved a VR. However, the optimal duration of treatment needs to be investigated in large prospective studies.

Procalcitonin in the setting of complicated postoperative course after liver transplantation

BACKGROUND

Orthotopic liver transplantation (OLT) is a treatment for end-stage liver disease. The shortage of available organs leads to the acceptance of marginal grafts, thereby increasing the risk of perioperative complications such as acute rejection, infection, and graft dysfunction Procalcitonin (PCT) has been shown to be a reliable marker for a complicated course after traumatic injury as well as in the courses of systemic inflammatory response syndrome and sepsis. The aim of our study was to evaluate PCT as an early prognostic marker for the occurrence of complication during the postoperative course after OLT.

METHOD

We analyzed PCT levels and clinical and paraclinical data of 32 patients who underwent 33 OLTs. The highest PCT was termed as peak-PCT. Patients were stratified into noncomplication and complication groups. Renal replacement therapy, respiratory insufficiency, postoperative bleeding, refractory ascites, pleural effusion, rejection, sepsis, and fatal outcome were defined as complications. A secondary stratification, using a peak-PCT of 5 ng/mL, was used to analyzed the risk of a complication. We also analyzed the course of PCT after OLT in each group.

RESULTS

The peak-PCT, which occurred between the first and third postoperative day in 30 patients, was followed by halving of the value every second day. Three subjects died because of sepsis. A constantly rising PCT or a secondary rise observed in 2 patients was associated with a fatal outcome. The noncomplication group included 18 patients, 8 of them showing a peakPCT <5 ng/mL and 10 above. The complication group included 14 patients who underwent 15 transplantations; Only 1 displayed a peakPCT <5 ng/mL. When the peak-PCT was >5 ng/mL, the odds ratio of a complication was 11.2 (95% Confidence interval, 10.81-11.59; P < .025). However, not before the 7th postoperative day was the course of mean PCT levels significantly different between the complication and noncomplication groups. In transplant patients, an elevation of PCT was observed only in the presence of bacterial infection and not rejection or wound infection. PCT rose during respiratory failure and sepsis, but not renal replacement therapy, ascites, pleural effusion, rejection, or bleeding.

CONCLUSION

PCT was a reliable marker. A decline was observed in 31 cases with subject, who both had fatal outcomes showing a constantly rising level. An initial high PCT indicated a poor prognosis; some members of the noncomplication group also had levels >15 ng/mL. The patients in the complication group showed a higher mean PCT, which was significant at 7 days, most probably because of the high variation among levels. Still, a peak-PCT >5 ng/mL showed an odds ratio of 11.2 for patients to experience a complication.

Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence

FoxM1 is a member of the Forkhead family of transcription factors and is implicated in inducing cell proliferation and some forms of tumorigenesis. It binds promoter regions with a preference for tandem repeats of a consensus ‘TAAACA’ recognition sequence. The affinity of the isolated FoxM1 DNA-binding domain for this site is in the micromolar range, lower than observed for other Forkhead proteins. To explain these FoxM1 features, we determined the crystal structure of its DNA-binding domain in complex with a tandem recognition sequence. FoxM1 adopts the winged-helix fold, typical of the Forkhead family. Neither ‘wing’ of the fold however, makes significant contacts with the DNA, while the second, C-terminal, wing adopts an unusual ordered conformation across the back of the molecule. The lack of standard DNA–‘wing’ interactions may be a reason for FoxM1’s relatively low affinity. The role of the ‘wings’ is possibly undertaken by other FoxM1 regions outside the DBD, that could interact with the target DNA directly or mediate interactions with other binding partners. Finally, we were unable to show a clear preference for tandem consensus site recognition in DNA-binding, transcription activation or bioinformatics analysis; FoxM1's moniker, ‘Trident’, is not supported by our data.

Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing

All organisms need to ensure that no DNA segments are rereplicated in a single cell cycle. Eukaryotes achieve this through a process called origin licensing, which involves tight spatiotemporal control of the assembly of prereplicative complexes (pre-RCs) onto chromatin. Cdt1 is a key component and crucial regulator of pre-RC assembly. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent DNA rereplication. Here, we address the mechanism of DNA licensing inhibition by Geminin, by combining X-ray crystallography, small-angle X-ray scattering, and functional studies in Xenopus and mammalian cells. Our findings show that the Cdt1:Geminin complex can exist in two distinct forms, a "permissive" heterotrimer and an "inhibitory" heterohexamer. Specific Cdt1 residues, buried in the heterohexamer, are important for licensing. We postulate that the transition between the heterotrimer and the heterohexamer represents a molecular switch between licensing-competent and licensing-defective states.

SPINE high-throughput crystallization, crystal imaging and recognition techniques: current state, performance analysis, new technologies and future aspects

This paper reviews the developments in high-throughput and nanolitre-scale protein crystallography technologies within the remit of workpackage 4 of the Structural Proteomics In Europe (SPINE) project since the project's inception in October 2002. By surveying the uptake, use and experience of new technologies by SPINE partners across Europe, a picture emerges of highly successful adoption of novel working methods revolutionizing this area of structural biology. Finally, a forward view is taken of how crystallization methodologies may develop in the future.

Eukaryotic expression: developments for structural proteomics

The production of sufficient quantities of protein is an essential prelude to a structure determination, but for many viral and human proteins this cannot be achieved using prokaryotic expression systems. Groups in the Structural Proteomics In Europe (SPINE) consortium have developed and implemented high‐throughput (HTP) methodologies for cloning, expression screening and protein production in eukaryotic systems. Studies focused on three systems: yeast (Pichia pastoris and Saccharomyces cerevisiae), baculovirus‐infected insect cells and transient expression in mammalian cells. Suitable vectors for HTP cloning are described and results from their use in expression screening and protein‐production pipelines are reported. Strategies for co‐expression, selenomethionine labelling (in all three eukaryotic systems) and control of glycosylation (for secreted proteins in mammalian cells) are assessed.

Implementation of semi-automated cloning and prokaryotic expression screening: the impact of SPINE

The implementation of high-throughput (HTP) cloning and expression screening in Escherichia coli by 14 laboratories in the Structural Proteomics In Europe (SPINE) consortium is described. Cloning efficiencies of greater than 80% have been achieved for the three non-ligation-based cloning techniques used, namely Gateway, ligation-indendent cloning of PCR products (LIC-PCR) and In-Fusion, with LIC-PCR emerging as the most cost-effective. On average, two constructs have been made for each of the approximately 1700 protein targets selected by SPINE for protein production. Overall, HTP expression screening in E. coli has yielded 32% soluble constructs, with at least one for 70% of the targets. In addition to the implementation of HTP cloning and expression screening, the development of two novel technologies is described, namely library-based screening for soluble constructs and parallel small-scale high-density fermentation.

SPINE bioinformatics and data-management aspects of high-throughput structural biology

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high‐throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high‐throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high‐throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

First steps towards effective methods in exploiting high-throughput technologies for the determination of human protein structures of high biomedical value

The EC 'Structural Proteomics In Europe' contract is aimed specifically at the atomic resolution structure determination of human protein targets closely linked to health, with a focus on cancer (kinesins, kinases, proteins from the ubiquitin pathway), neurological development and neurodegenerative diseases and immune recognition. Despite the challenging nature of the analysis of such targets, approximately 170 structures have been determined to date. Here, the impact of high-throughput technologies, such as parallel expression of multiple constructs, the use of standardized refolding protocols and optimized crystallization screens or the use of mass spectrometry to assist sample preparation, on the structural biology of mammalian protein targets is illustrated through selected examples.

SPINE workshop on automated X-ray analysis: a progress report

The Structural Proteomics In Europe (SPINE) consortium contained a workpackage to address the automated X-ray analysis of macromolecules. The aim of this workpackage was to increase the throughput of three-dimensional structures while maintaining the high quality of conventional analyses. SPINE was able to bring together developers of software with users from the partner laboratories. Here, the results of a workshop organized by the consortium to evaluate software developed in the member laboratories against a set of bacterial targets are described. The major emphasis was on molecular-replacement suites, where automation was most advanced. Data processing and analysis, use of experimental phases and model construction were also addressed, albeit at a lower level.

wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models

wARP is a procedure that substantially improves crystallographic phases (and subsequently electron-density maps) as an additional step after density-modification methods such as solvent flattening and averaging. The initial phase set is used to create a number of dummy atom models which are subjected to least-squares or maximum-likelihood refinement and iterative model updating in an automated refinement procedure (ARP). Averaging of the phase sets calculated from the refined output models and weighting of structure factors by their similarity to an average vector results in a phase set that improves and extends the initial phases substantially. An important requirement is that the native data have a maximum resolution beyond approximately 2.4 A. The wARP procedure shortens the time-consuming step of model building in crystallographic structure determination and helps to prevent the introduction of errors.

ARP/wARP and molecular replacement

The aim of ARP/wARP is improved automation of model building and refinement in macromolecular crystallography. Once a molecular-replacement solution has been obtained, it is often tedious to refine and rebuild the initial (search) model. ARP/wARP offers three options to automate that task to varying extents: (i) autobuilding of a completely new model based on phases calculated from the molecular-replacement solution, (ii) updating of the initial model by atom addition and deletion to obtain an improved map and (iii) docking of a structure onto a new (or mutated) sequence, followed by rebuilding and refining the side chains in real space. A few examples are presented where ARP/wARP made a considerable difference in the speed of structure solution and/or made possible refinement of otherwise difficult or uninterpretable maps. The resolution range allowing complete autobuilding of protein structures is currently 2.0 A, but for map improvement considerable advances over more conventional refinement techniques are evident even at 3.2 A spacing.

Structure elucidation of beta-mannanase: from the electron-density map to the DNA sequence

The crystal structure of affinity-purified Thermomonospora fusca beta-mannanase has been solved despite the lack of the major part of the amino-acid sequence. A high-quality electron-density map allowed the identification of a stretch of eight amino acids close to the C-terminus which was used to design a degenerate downstream PCR primer. Together with a specific primer previously derived from the N-terminus, 95.7% of the mannanase gene sequence was obtained from genomic T. fusca DNA by PCR. The structure-derived sequence was then compared with the DNA-derived sequence and corrected when necessary. Applying the presented protocol, there was no need to manually build a model at an early stage of structure determination, an erroneous and tedious process, especially in the absence of the amino-acid sequence. Using the DNA sequence information and the current version of ARP/wARP, 281 residues, or 93% of the polypeptide chain (including side chains), were built and refined to an R factor of 16.5% without any manual intervention.

Current state of automated crystallographic data analysis

A goal of structural biology--and of structural genomics in particular--is to improve the underlying methodology for high-throughput determination of three-dimensional structures of biological macromolecules. Here we address issues related to the development, automation and streamlining of the process of macromolecular X-ray crystal structure solution.

The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch

DNA mismatch repair ensures genomic integrity on DNA replication. Recognition of a DNA mismatch by a dimeric MutS protein initiates a cascade of reactions and results in repair of the newly synthesized strand; however, details of the molecular mechanism remain controversial. Here we present the crystal structure at 2.2 A of MutS from Escherichia coli bound to a G x T mismatch. The two MutS monomers have different conformations and form a heterodimer at the structural level. Only one monomer recognizes the mismatch specifically and has ADP bound. Mismatch recognition occurs by extensive minor groove interactions causing unusual base pairing and kinking of the DNA. Nonspecific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. The interleaved nucleotide-binding sites are located far from the DNA. Mutations in human MutS alpha (MSH2/MSH6) that lead to hereditary predisposition for cancer, such as hereditary non-polyposis colorectal cancer, can be mapped to this crystal structure.

The X-ray crystal structure of neuronal Sec1 from squid sheds new light on the role of this protein in exocytosis

BACKGROUND

Sec1-like molecules have been implicated in a variety of eukaryotic vesicle transport processes including neurotransmitter release by exocytosis. They regulate vesicle transport by binding to a t-SNARE from the syntaxin family. This process is thought to prevent SNARE complex formation, a protein complex required for membrane fusion. Whereas Sec1 molecules are essential for neurotransmitter release and other secretory events, their interaction with syntaxin molecules seems to represent a negative regulatory step in secretion.

RESULTS

Here we report the X-ray crystal structure of a neuronal Sec1 homologue from squid, s-Sec1, at 2.4 A resolution. Neuronal s-Sec1 is a modular protein that folds into a V-shaped three-domain assembly. Peptide and mutagenesis studies are discussed with respect to the mechanism of Sec1 regulation. Comparison of the structure of squid s-Sec1 with the previously determined structure of rat neuronal Sec1 (n-Sec1) bound to syntaxin-1a indicates conformational rearrangements in domain III induced by syntaxin binding.

CONCLUSIONS

The crystal structure of s-Sec1 provides the molecular scaffold for a number of molecular interactions that have been reported to affect Sec1 function. The structural differences observed between s-Sec1 and the structure of a rat n-Sec1-syntaxin-1a complex suggest that local conformational changes are sufficient to release syntaxin-1a from neuronal Sec1, an active process that is thought to involve additional effector molecule(s).